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A set of plastid microsatellite loci for the genus Dyckia (Bromeliaceae) derived from 454 pyrosequencing

Authors:

Abstract

Unlabelled: • Premise of the study: Phylogeographical analyses of Dyckia (Bromeliaceae) suffer from low levels of sequence variation. Plastid microsatellite markers were developed to achieve a better-resolved genus-wide plastid genealogy of Dyckia. • Methods and results: Approximately 84% of the D. marnier-lapostollei plastome was sequenced using 454 technology. Flanking primer pairs were designed for 34 out of 36 chloroplast simple sequence repeats (cpSSRs) detected, and 12 loci were further characterized by genotyping Dyckia samples at the level of populations and species. Three, five, and six cpSSRs were polymorphic among four individuals of D. limae, 12 individuals of D. dissitiflora, and 12 of D. pernambucana, respectively, with two to three alleles per locus and species. All loci were polymorphic among 19 different Dyckia species, with three to 10 alleles per locus. Ten primer pairs cross-amplified with bromeliad genera from five subfamilies. • Conclusions: The set of 12 cpSSR markers provides a toolbox to analyze phylogeographical patterns of Dyckia species.
e470
American Journal of Botany: e470–e473, 2012; http://www.amjbot.org/ © 2012 Botanical Society of America
American Journal of Botany: e470–e473. 2012.
The genus Dyckia Schult. f. (Bromeliaceae) currently com-
prises 147 described species of xerophytic, terrestrial, or epi-
lithic rosette plants with showy yellow, red, or orange fl owers
( Smith and Downs, 1974 ). The genus is distributed across east-
ern South America, with a center of diversity in the cerrado
biome of Brazil and adjacent countries. Species of Dyckia and
of its closest relative Encholirium Mart. ex Schult. f. typically
inhabit azonal, arid, or rupicolous habitats that are character-
ized by poor soil, little water supply, high temperatures, and
strong sun exposure. Pollination is mainly by hummingbirds
and insects. Fruits are capsules that release winged, wind-dis-
persed seeds upon maturity ( Smith and Downs, 1974 ).
Little is known about infrageneric relationships within Dy-
ckia , the genetic structure and variation within its species, and
the mechanisms of speciation. This paucity of information is
in part due to the fact that many Dyckia species are rare and
narrow endemics, which are barely represented in herbaria
and living collections. Some species are even known from
their type locality only. Another problem is the high degree of
intraspecifi c morphological plasticity, which makes species
delimitation in Dyckia notoriously diffi cult. We have initiated
a genus-wide molecular phylogenetic study of Dyckia , based
on plastid and nuclear DNA sequences. Our preliminary results
indicate very low levels of plastid sequence divergence, sug-
gesting a young age of the genus (Krapp, unpublished data).
Whereas chloroplast haplotypes are often shared between species,
haplotype networks based on plastid DNA show a pronounced
geographical pattern across the distributional range of the genus.
Chloroplast simple sequence repeats (cpSSRs), also called
chloroplast microsatellites, are among the most sensitive tools
for evaluating plastid DNA variation ( Ebert and Peakall, 2009 ).
To achieve a better-resolved genus-wide plastid phylogeogra-
phy of Dyckia , we developed a set of 12 polymorphic cpSSR
markers based on de novo 454 sequencing.
METHODS AND RESULTS
Total genomic DNA was isolated from one individual plant of Dyckia
marnier-lapostollei L. B. Sm. var. estevesii Rauh from Goiania, central Brazil
(see Appendix 1), using a modifi ed cetyltrimethylammonium bromide
(CTAB) procedure ( Tel-Zur et al., 1999 ). This species was chosen because its
plastid haplotype takes a central position in a statistical parsimony network,
suggesting an ancestral state within the genus (Krapp, unpublished results).
Fragmentation of a 5- μ g DNA aliquot by nebulization, preparation of bar-
coded libraries, and shotgun sequencing on a Roche 454 GS-FLX with the
Titanium Sequencing Kit XLR70 and the Titanium PicoTiterPlate Kit (Roche
Diagnostics, Penzberg, Germany) were performed as described previously
( Wöhrmann et al., 2012a ). Altogether, 59 624 reads were obtained from three
independent runs. The proportion of a single 454 sequencing lane devoted to
D. marnier-lapostollei was 4.2%, 2.1%, and 4.1% in the fi rst, second, and
third run, respectively. Sequences of plastid origin were identifi ed using the
BLAST function of the software package Geneious ( Drummond et al., 2010 ).
The fully sequenced plastome of Typha latifolia L. ( Guisinger et al., 2010 )
1 Manuscript received 23 March 2012; revision accepted 19 June 2012.
The authors thank J. Peters, N. Schütz, and the Botanical Gardens of
Heidelberg, Bonn, and Vienna for providing plant material, as well as R. B.
Louzada, G. Cruz, and A. M. Wanderley for help during fi eld work. F.K. and
D.S.B.P. are supported by fellowship grants of the Otto-Braun-Fonds
(Melsungen) and the Fundação de Amparo à Ciência e Tecnologia do Estado
de Pernambuco (FACEPE), respectively. This work was supported by
PNADB/CAPES and DAAD/CAPES in the frame of a PROBRAL project.
5 Author for correspondence: weising@uni-kassel.de
doi:10.3732/ajb.1200153
AJB PRIMER NOTES & PROTOCOLS IN THE PLANT SCIENCES
A SET OF PLASTID MICROSATELLITE LOCI FOR THE
GENUS DYCKIA (BROMELIACEAE) DERIVED FROM 454
PYROSEQUENCING
1
F LORIAN K RAPP 2 , T INA W ÖHRMANN 2 , D IEGO SOTERO DE BARROS P INANGÉ 3 , A NA MARIA
B ENKO-ISEPPON 3 , B RUNO H UETTEL 4 , AND KURT W EISING 2,5
2 Plant Molecular Systematics, Department of Sciences, University of Kassel, D-34132 Kassel, Germany;
3 Genetics Department,
CCB, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego 1235, 50670-420, Recife, Pernambuco, Brazil; and
4 Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
Premise of the study: Phylogeographical analyses of Dyckia (Bromeliaceae) suffer from low levels of sequence variation.
Plastid microsatellite markers were developed to achieve a better-resolved genus-wide plastid genealogy of Dyckia .
Methods and Results: Approximately 84% of the D. marnier-lapostollei plastome was sequenced using 454 technology. Flank-
ing primer pairs were designed for 34 out of 36 chloroplast simple sequence repeats (cpSSRs) detected, and 12 loci were further
characterized by genotyping Dyckia samples at the level of populations and species. Three, fi ve, and six cpSSRs were polymor-
phic among four individuals of D. limae , 12 individuals of D. dissitifl ora , and 12 of D. pernambucana , respectively, with two
to three alleles per locus and species. All loci were polymorphic among 19 different Dyckia species, with three to 10 alleles per
locus. Ten primer pairs cross-amplifi ed with bromeliad genera from fi ve subfamilies.
Conclusions: The set of 12 cpSSR markers provides a toolbox to analyze phylogeographical patterns of Dyckia species.
Key words: Bromeliaceae; cpSSR; Dyckia ; plastome; population genetics.
e471
December 2012] AJB PRIMER NOTES & PROTOCOLSDYCKIA CPSSRS
clamp of up to three nucleotides at the 3 end. For three loci (DSSR-L01,
DSSR-L04, and DSSR-L06; Table 1 ) , consensus primers were derived from
alignments of the D. marnier-lapostollei sequence with sequence data previ-
ously generated by Sanger sequencing of the same loci in other Dyckia spe-
cies (Krapp, unpublished data).
Primer functionality was initially tested on a single accession each of
D. marnier-lapostollei , D. dissitifl ora Schult. f., and D. pernambucana
L. B. Sm. PCRs were carried out in 10- μ L volumes using a Biometra T1-cycler
or a Biometra T-Gradient cycler (Biometra GmbH, Göttingen, Germany), using
was taken as a reference. A total of 3826 plastid reads were assembled into 77
contigs and 12 singletons, which together represent 113 449 bases of the D.
marnier-lapostollei plastome (counting the two inverted repeats only once).
This corresponds to an overall coverage of ~84%, when compared to the
T. latifolia plastome. A total of 36 mononucleotide repeats with 10 bases were
detected (181 with 7 bases) using the FIND function of PhyDE ( Müller
et al., 2010 ). Besides two short dinucleotide repeats, each with an (AT)
5
motif, no other types of SSRs were observed. Flanking primer pairs were
designed by eye for 34 loci, with a default length of 20 nucleotides and a GC
T ABLE 1. Characteristics of 12 chloroplast microsatellite primer pairs developed in Dyckia marnier-lapostollei var. estevesii .
Locus Primer sequences (5 –3 ) Position Repeat motif Size (bp) GenBank accession no.
a
DSSR-L01 F: GTCAATTTTCAAGTTCAGCC atp B- rbc L (T)
13 C(A) 10 75 JQ743912
R: TCACGATTTCATCTACTTGC intergenic
DSSR-L04 F: AAAGGATGAGATCAATTCGG ndh A (T)
9 * 94 JQ743913
R: AAGATACATCGGAAAGTCCC intronic
DSSR-L06 F: ATTGATTGAATAAACCGGGG trn K-UUU- rps 16 (T)
13 77 JQ743914
R: TAAATAAGAAATTGGAATGG intergenic
DSSR-N01 F: GTTCCCAGTAAGAACCAACC rpo C1 (T)
14 102 JQ743915
R: CTCAATAATTTCACATTTCC intronic
DSSR-N04 F: GAAATCAATGTGTCGATTCC clp P (T)
11 87 JQ743916
R: TTTNAATAGAAAGAAGACCC intronic
DSSR-N05 F: TGAGATGAGTTTTGGCTCCC clp P (A)
12 85 JQ743917
R: AACAATACATCAATGATAGG intronic
DSSR-N07 F: ATTATATACATCTGAAACCC trn P-UGG- psa J (A)
13 74 JQ743918
R: CTTCCTCCTGAGCATTACGG intergenic
DSSR-N10 F: TNAATCAATATGGCGAAGGC clp P (T)
10 79 JQ743919
R: ATTCCCTCACGCTTGGCGCC intronic
DSSR-N11 F: ATAGATAAAATTATCGGGCC ndh G- ndh I (A)
18 100 JQ743920
R: AAATTTAAACTACATATTCC intergenic
DSSR-N15 F: CTTCCATTTATCCATATCCC rpl 16 (T)
11 64 JQ743921
R: AAAATAAATCTGATTATGGG intronic
DSSR-N16 F: TTATACCAAATGATCAATCG rpl 16- rps 3 (T)
13 90 JQ743922
R: ACTCTTTCATTCTTTTTCCG intergenic
DSSR-N18 F: AAATAGGTAATCTATTCCCC psb K- psb I (A)
15 63 JQ743923
R: GTAAGCATTACACAATCTCC intergenic
a GenBank accession numbers of the sequences on which the primers are based.
* The SSR motif at DSSR-L04 had only nine T residues in D. marnier-lapostollei , but had up to 14 T residues in other Dyckia species for which sequence
data were available for primer design.
T ABLE 2. Observed allele sizes at 12 chloroplast microsatellite loci in three populations of D. dissitifl ora and D. pernambucana and one population of
D. limae , allele numbers and size range in 19 different Dyckia species (one individual each), and cross-amplifi cation in eight additional genera of
Bromeliaceae (see Appendix 1 ).
Allele sizes
D. dissitifl ora D. pernambucana D. limae 19 Dyckia species
Cross-amplifi cation in other bromeliad
genera
Locus
Cachoeira*
( N = 4)
Lajes*
( N = 4)
Morrão*
( N = 4)
Aldeia*
( N = 4)
Brejo*
( N = 4)
Papagaio*
( N = 4)
Jerusalém*
( N = 4) No. of alleles
Size range
(bp) En De Fo Pi Pu An He Ti
DSSR-L01 75 75, 76 75, 76 77 75, 76 77 76, 77 9 72–80 + + + + + + +
DSSR-L04 98 98 98 99 97 98 99 6 94–99 + + + + + + + +
DSSR-L06 79 79, 80 79, 80 78 78 78 78 8 73–82 + + + + + + + +
DSSR-N01 102 102 102 102 102 102 102 8 98–109 + + + + + + + +
DSSR-N04 91 91 91 91 92 91 91 8 87–98 + + — —
DSSR-N05 86 86 86 85, 86 85, 86 86 85, 86 4 84–87 + + + + + + + +
DSSR-N07 74 74 74 74 74 74 74 5 71–75 + + — + + + + +
DSSR-N10 81 79 79, 81 79 79 79 79 3 79–81 + + + + + + + +
DSSR-N11 99 96 100 99 97 98 98 98 10 94–104 + + + +
DSSR-N15 65 65 65 65 65 65 65 3 64–66 + + + + + + + +
DSSR-N16 90 90 90 90 90 90 90 5 87–91 + + + + + + + +
DSSR-N18 68 72, 73 68, 72 66 66 67 62, 66 9 62–73 + + + + + + + +
Note : + = amplifi cation; — = no amplifi cation; An = Ananas (Bromelioideae); De = Deuterocohnia ; En = Encholirium ; Fo = Fosterella ; Pi = Pitcairnia
(all Pitcairnioideae); He = Hechtia (Hechtioideae); Pu = Puya (Puyoideae); Ti = Tillandsia (Tillandsoideae).
* Locality information for the populations is provided in Appendix 1 .
Single PCR product in the expected size range.
e472 AMERICAN JOURNAL OF BOTANY [Vol. 0
the indirect fl uorescence labeling procedure described by Schuelke (2000) .
Each assay contained approximately 1 ng of template DNA, 1 × Mango- Ta q
reaction buffer (Bioline, Taunton, Massachusetts, USA), 1.5 mM MgCl
2 , 0.2 mM
of each dNTP, 0.04 μ M forward primer carrying a 5 -M13 tail, 0.16 μ M of M13
forward primer with fl uorescent 5 -IRD700 modifi cation, 0.16 μ M unlabeled
reverse primer, 0.5 μ g/ μ L BSA, and 0.05 U Mango- Ta q DNA polymerase (Bioline).
All loci were amplifi ed using a standard PCR program with an initial denatur-
ation at 80 ° C for 5 min, followed by 30 cycles of denaturation at 94 ° C for 1
min, primer annealing at 52 ° C for 1 min, and elongation at 65 ° C for 2 min. Final
extension was performed at 65 ° C for 10 min. Samples were electrophoresed on
denaturing 6% polyacrylamide gels in 1 × TBE buffer, using an automated
sequencer (Li-Cor 4200 IR
2 ; Li-Cor Biosciences, Bad Homburg, Germany).
Fragment sizes were determined by visual examination with the help an external
size standard, as outlined by Wöhrmann et al. (2012a) . Allele sizes were validated
by repeated PCRs of subsets of samples using either Mango- Ta q polymerase or
a set of proofreading polymerases (Long High Fidelity Enzyme Mix; Rovalab,
Teltow, Germany), following the protocol supplied by the manufacturer.
The 12 most polymorphic cpSSR loci were used to genotype (1) population
samples from D. limae L. B. Sm., D. dissitifl ora , and D. pernambucana ; (2) single
accessions from 16 additional Dyckia species; and (3) one or two species each
of eight bromeliad genera belonging to fi ve subfamilies. Dyckia dissitifl ora was
chosen as an example of a Dyckia species with a relatively large distribution
range across Brazil, whereas D. limae and D. pernambucana were taken as a
typical example of two species that are not clearly distinguishable by morpho-
logical characters. Locus characteristics, primer sequences, and GenBank
accession numbers of these 12 markers are summarized in Table 1 , fragment
sizes for all samples and loci are compiled in Table 2 , and all plant materials
used in this study are listed in Appendix 1.
Three, ve, and six cpSSR loci were polymorphic among four individuals of
D. limae , 12 individuals from three populations of D. dissitifl ora , and 12 indi-
viduals from three populations of D. pernambucana , respectively ( Table 2 ).
Two to three alleles were observed per locus and species. All loci were highly
polymorphic at the species level, with three to 10 alleles per locus across 19
Dyckia species ( Table 2 ). Allele size distributions were generally compatible,
with a variable number of mononucleotide repeats being the molecular basis for
size variation. Overall, only six out of 540 individual PCRs performed with any
Dyckia species failed. All loci produced single PCR fragments within the ex-
pected size range in the closely related genera Encholirium and Deuterocohnia
Mez, and nine of the 12 primer pairs successfully cross-amplifi ed in six other
genera from fi ve subfamilies of Bromeliaceae ( Table 2 ).
CONCLUSIONS
The set of 12 novel cpSSR markers presented here provides
a promising toolbox for reconstructing plastid genealogies and
elucidating phylogeographical patterns within Dyckia . In con-
junction with nuclear SSR markers that are currently being devel-
oped in our group ( Wöhrmann et al., 2012b ), the cpSSRs are also
promising candidates for population genetic analyses in D. dis-
sitifl ora , D. limae , D. pernambucana , and probably many other
Dyckia species. Primer binding sites appear to be well-conserved
among Bromeliaceae, suggesting that the 12 cpSSR markers
may be applicable for genetic studies throughout the family.
LITERATURE CITED
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S MITH , L. B. , AND R. J. DOWNS . 1974 . Pitcairnioideae (Bromeliaceae).
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T EL-ZUR , N . , S . A BBO , D . M YSLABODSKI , AND Y . M IZRAHI . 1999 . Modifi ed
CTAB procedure for DNA isolation from epiphytic cacti of the genera
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W ÖHRMANN , T . , N . W AGNER , F . K RAPP , B . H UETTEL , AND K . W EISING .
2012a . Development of microsatellite markers in Fosterella rusbyi
(Bromeliaceae) using 454 pyrosequencing. American Journal of
Botany 99 : e160 – e163 .
W ÖHRMANN , T. , D. S. B. PINANGÉ , F . K RAPP , A. M. BENKO-ISEPPON ,
B . H UETTEL , AND K . W EISING . 2012b . Development of 15 nuclear micro-
satellite markers in the genus Dyckia (Pitcairnioideae; Bromeliaceae)
using 454 pyrosequencing. Conservation Genetics Resources DOI:
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e473
December 2012] AJB PRIMER NOTES & PROTOCOLSDYCKIA CPSSRS
A PPENDIX 1 . Plant material used for this study.
Species Collector (Herbarium)
a Location
b GPS coordinates
Dyckia dissitifl ora Schult. f. A. M. Iseppon, Pinangé, D. & Cruz, G. 1605 (UFP) Cachoeira “Ferro Doido,” Bahia (BR) −11.6279; −41.0005
Pop. Cachoeira ( N = 4)
Dyckia dissitifl ora Schult. f. A. M. Iseppon, Pinangé, D. & Cruz, G. 1598 (UFP) Lajes, Bahia (BR) −11.6010; −41.1645
Pop. Lajes ( N = 4)
Dyckia dissitifl ora Schult. f. A. M. Iseppon, Pinangé, D. & Cruz, G. 1562 (UFP) Morrão, Bahia (BR) −11.5901; −41.2072
Pop. Morrão ( N = 4)
Dyckia limae L. B. Sm. A. M. Wanderley s.n. (UFP) Serra de Jerusalém, Pernambuco (BR) −8.5837; −37.2384
Pop. Jerusalém ( N = 4)
Dyckia pernambucana L. B. Sm. D. Pinangé et al. DCKB/09.2009 (UFP) Aldeia Couro d’Anta, Pernambuco (BR) −8.3254; −36.7562
Pop. Aldeia ( N = 4)
Dyckia pernambucana L. B. Sm. D. Pinangé et al. DKCA/09.2009 (UFP) Brejo da Madre de Deus, Pernambuco
(BR)
−8.1894; −36.3931
Pop. Brejo ( N = 4)
Dyckia pernambucana L. B. Sm. A. M. Wanderley s.n. (UFP) Pico do Papagaio, Pernambuco (BR) −7.8228; −38.0554
Pop. Papagaio ( N = 4)
Dyckia aff. brevifolia Baker P. Braun 840 (HD) Itacambira, Minas Gerais (BR) −17.0667; −43.3000
Dyckia estevesii Rauh P. Braun s.n. (HD) BR NA
Dyckia ferox Mez W. Rauh 64237 (HD) Cerro Colorado, Cordoba (RA) −30.1000; −63.9333
Dyckia goehringii E. Gross & Rauh W. Rauh 67622 (HD) Diamantina, Minas Gerais (BR) −18.2500; −43.6000
Dyckia granmogulensis Rauh W. Rauh 56484 (HD) Grão Mogol, Minas Gerais (BR) −16.5667; −42.9000
Dyckia aff.
ibiramensis Reitz L. Horst 1287 (HD) Diamantina, Minas Gerais (BR) −18.2500; −43.6000
Dyckia leptostachya Baker H. Amerhauser s.n. (WU) Caacupé, Cordillera (PY) −25.3833; −57.1500
Dyckia lindevaldae Rauh P. Braun BR 691 (HD) Alto Paraiso, Goiás (BR) −14.1167; −47.5167
Dyckia macedoi L. B. Sm. R. B. Louzada, Pinangé, D. & Medeiros, M. 151 (SP) Santana do Riacho, Minas Gerais (BR) −19.3539; −43.6237
Dyckia marnier-lapostollei var.
estevesii Rauh
L. Horst 5 (HD) Goiania, Goiás (BR) −16.6667; −49.2667
Dyckia marnier-lapostollei L. B. Sm. L. Horst 4 (HD) Cristalina, Goiás (BR) −16.7500; −47.6000
Dyckia microcalyx Baker W. Till 6020 (WU) Cerros Acahay, Paraguari (PY) −25.9167; −57.1500
Dyckia aff. pumila L. B. Sm. P. Braun BR 696 (HD) Ponte Branca, Mato Grosso (BR) −16.4500; −52.6667
Dyckia remotifl ora var. indet.
Otto & A. Dietr.
L. Horst s.n. (HD) BR NA
Dyckia tobatiensis Hassl. W. & S. Till 6050 (WU) Tobati, Cordillera (PY) −25.2500; −57.0667
Dyckia velascana Mez W. & S. Till 5012 (WU) Ascochinga, Cordoba (RA) −30.9500; −64.2667
Dyckia vestita Hassl. W. & S. Till 6018 (WU) Paraguari, Paraguari (PY) −25.6333; −57.1500
Encholirium horridum L. B. Sm. W. Schindhelm s.n. (HD) Pedra Azul, Minas Gerais (BR) −15.9867; −41.4069
Encholirium magalhaesii L. B. Sm. s.n. (BONN) BR NA
Deuterocohnia brevispicata
Rauh & L. Hrom.
N. Schütz 06/028 (FR) Florida, Santa Cruz (BOL) −18.0154; −64.1001
Deuterocohnia glandulosa E. Gross N. Schütz 06/019 (FR) Ipati, Santa Cruz (BOL) −19.7063; −63.6521
Fosterella villosula (Harms) L. B. Sm. J. Peters 06.0105 (HD) Cochabamba, Cochabamba (BOL) −17.0611; −65.6444
Fosterella weddelliana (Brongn. ex Baker)
L. B. Sm.
M. Miyagawa s.n. (HD) Solacana (BOL) NA
Pitcairnia feliciana (A. Chev.) Harms &
Mildbr.
I. Ebert & D. Bangoura s.n. ex coll. P. Bak (WU) RG NA
Pitcairnia heterophylla (Lindl.) Beer K. Senghas O-11230 (HD) Cruz de Ocotte, Guerrero (MEX) 17.5500; 99.8833
Puya ferruginea (Ruiz & Pav.) L. B. Sm. W. Rauh s.n. (HD) Rio Marañon (PE) NA
Puya herzogii Wittm. T. Krömer 6581 (HD) Carrasco, Cochabamba (BOL) −17.1933; −64.9731
Ananas ananassoides (Baker) L. B. Sm. P. Maas s.n. (HD) Est. Amazonas (BR) NA
Hechtia caerulea (Matuda) L. B. Sm. W. Rauh s.n. (HD) Est. Mexico (MEX) NA
Tillandsia usneoides (L.) L
Q6 . W. Rauh s.n. (HD) Yungas Cachi (RA) NA
Note : N = population size Q7 ; NA = not available Q8 .
a Herbaria: BONN = University of Bonn; FR = Senckenberg Research Institute, Frankfurt; HD = Botanical Garden of Heidelberg; SP = Instituto de
Botânica; São Paulo; UFP = Universidade Federal de Pernambuco; WU = University of Vienna.
b BOL = Bolivia; BR = Brazil; MEX = Mexico; PE = Peru; PY = Paraguay; RA = Argentina; RG = Guinea.

Supplementary resources (12)

... While developing custom primers for new SSRs can be cost prohibitive (Oliveira et al. 2006), it is possible to use primers previously developed for closely related species in a process called cross-amplification (Oliveira et al. 2006). Previous studies involving the development and crossamplification of SSRs markers in Bromeliaceae have primarily focused on species of the Tillandsioideae (Boneh et al. 2003;Palma-Silva et al. 2007;Lavor et al. 2013;Neri et al. 2015) and Pitcairnioideae subfamilies (Sarthou et al. 2003;Paggi et al. 2008;Krapp et al. 2012;Miranda et al. 2012;Wöhrmann et al. 2012Wöhrmann et al. , 2013Zanella et al. 2012;Hmeljevski et al. 2013). Few studies have focused on the species in the subfamily Bromelioideae (Goetze et al. 2013;Krapp et al. 2013;Aoki-Gonçalves et al. 2014). ...
... While developing custom primers for new SSRs can be cost prohibitive (Oliveira et al. 2006), it is possible to use primers previously developed for closely related species in a process called cross-amplification (Oliveira et al. 2006). Previous studies involving the development and crossamplification of SSRs markers in Bromeliaceae have primarily focused on species of the Tillandsioideae (Boneh et al. 2003;Palma-Silva et al. 2007;Lavor et al. 2013;Neri et al. 2015) and Pitcairnioideae subfamilies (Sarthou et al. 2003;Paggi et al. 2008;Krapp et al. 2012;Miranda et al. 2012;Wöhrmann et al. 2012Wöhrmann et al. , 2013Zanella et al. 2012;Hmeljevski et al. 2013). Few studies have focused on the species in the subfamily Bromelioideae (Goetze et al. 2013;Krapp et al. 2013;Aoki-Gonçalves et al. 2014). ...
... The cross-amplification was moderate in both Cryptanthus species, about 64% of the loci tested were amplified, and about 35% of the loci tested were polymorphic. The cross-amplification in the three subfamilies tested confirms that the loci can be transferred between the different Cross-amplification of nuclear microsatellite markers in two species of Cryptanthus Otto… species from different subfamilies of Bromeliaceae (Palma-Silva et al. 2007;Paggi et al. 2008;Krapp et al. 2012;Zanella et al. 2012;Goetze et al. 2013;Lavor et al. 2013;Aoki-Gonçalves et al. 2014;Neri et al. 2015). ...
Article
Full-text available
Thirty-eight nuclear microsatellite loci originally developed for Aechmea caudata Lindm., Orthophytum ophiuroides Louzada & Wand., Pitcairnia albiflos Herb., Vriesea gigantea (Gaud.) and V. simplex (Vell.) Beer were tested in Cryptanthus burle-marxii Leme and C. zonatus (Vis.) Vis. Of the 38 loci tested, 13 were polymorphic. Ten polymorphic microsatellite loci were selected to be amplified and genotyped in one population each of C. burle-marxii and C. zonatus. The observed and expected heterozygosity per locus in the C. burle-marxii population ranged from 0.050 to 0.850 and 0.050 to 0.770, respectively. In C. zonatus, the observed and expected heterozygosity per locus ranged from 0.167 to 0.846 and 0.290 to 0.692, respectively. The O. ophiuroides locus Op52 for the C. zonatus population and P. albiflos locus PaC05 for the two species showed significant departure from HWE. These ten polymorphic loci tested will be used to assess the genetic diversity and structure of the two species of Cryptanthus.
... We used ten nuclear microsatellite loci, four isolated from Ananas comosus (L.) Merr. ( Krapp et al., 2012) were used to identify and characterize plastid DNA haplotypes in a subset of 187 individuals. All markers used in this study were chosen based on cross-amplification tests of markers for Bromeliaceae. ...
... For marker N18, we used 0.05 ρmol of forward primer and 2.0 ρmol each of reverse and universal M13 primers. The cycling program described by Krapp et al. (2012) was followed for the plastid markers. The nuclear and plastid alleles were resolved on an ABI 3500 DNA Analyzer Sequencer (Applied Biosystems) and sized against the GS500 LIZ molecular size standard (Applied Biosystems) using Genemarker demo v.1.97 ...
Article
Recently diversified taxa commonly do not show complete reproductive isolation, and thus they represent an interesting model for studying the occurrence of hybridization and its influence on the integrity of species. In this study, we aim to elucidate the occurrence of hybridization and discuss species boundaries between three Aechmea spp. (Bromeliaceae) from southern Brazil. To achieve these aims, we used ten nuclear and six plastid microsatellite loci. We also investigated morphological and ecological differentiation and reproductive compatibility through interspecific cross-pollination experiments with these species. Molecular analyses confirmed the occurrence of hybridization between the three species, but interspecific gene flow was higher between A. comata and A. kertesziae than between A. comata and A. caudata. These Aechmea spp. showed morphological differentiation, and the results of the artificial interspecific crosses indicated that they can intercross. Aechmea caudata and A. kertesziae show distinct microhabitat preferences, whereas A. comata thrives in a microhabitat that is also inhabited by the other species. Despite the potential reproductive barriers being weak, especially those between A. comata and A. kertesziae, they may maintain the boundaries between these species and their integrity in sympatric populations.
... In addition, six plastid microsatellite markers were amplified to study the haplotype variation among species. The plastid microsatellite markers used in this study were isolated from Dyckia marnierlapostollei L.B.Smith (DSSR-L01, DSSR-L04, DSSR-N01, DSSR-N07, DSSR-N16 and DSSR-N11; Krapp et al., 2012). Polymerase chain reaction (PCR) and genotyping were performed in a Veriti 96-well thermal cycler (Applied Biosystems, Foster City, CA, USA), based on Zanella et al. (2012b) for nuclear microsatellite markers and according to Krapp et al. (2012) for plastid microsatellite markers. ...
... The plastid microsatellite markers used in this study were isolated from Dyckia marnierlapostollei L.B.Smith (DSSR-L01, DSSR-L04, DSSR-N01, DSSR-N07, DSSR-N16 and DSSR-N11; Krapp et al., 2012). Polymerase chain reaction (PCR) and genotyping were performed in a Veriti 96-well thermal cycler (Applied Biosystems, Foster City, CA, USA), based on Zanella et al. (2012b) for nuclear microsatellite markers and according to Krapp et al. (2012) for plastid microsatellite markers. Nuclear and plastid simple sequence repeat (SSR) markers were resolved on an ABI 3500 Genetic Analyzer (Applied Biosystems) via comparison with a GS500 LIZ molecular size standard (Applied Biosystems) using GeneMarker demo v.1.97 ...
Article
When related species are distributed in sympatric populations, hybridization may occur. Likewise, one or more of these species may have arisen through historical hybridization between taxa. Here, we aim to elucidate the occurrence of hybridization among three Dyckia spp. (Bromeliaceae) from southern Brazil. We used seven nuclear and six plastid microsatellite loci to assess patterns of genetic diversity, population structure and hybridization in the three species. Furthermore, we performed manual crosses between species to test compatibility and fertility. The results showed that Dyckia julianae has an intermediate molecular profile, low gene flow occurs between Dyckia hebdingii and Dyckia choristaminea and higher gene flow occurs between D. julianae and the other two species. Plastid microsatellites identified 12 haplotypes that are shared among the species. The manual crosses between D. julianae and the other two species produced viable seeds, but no crosses between D. hebdingii and D. choristaminea generated fruits. Our data suggest that the reproductive barrier between D. julianae and the other two species is permeable. Further investigation into the hybrid origin hypothesis of D. julianae should be undertaken, as well as the mechanisms involved in reproductive isolation between D. hebdingii and D. choristaminea.
... Four chloroplast microsatellite markers (hereafter "cpSSRs") originally developed for Dyckia marnier-lapostollei var. estevesii (Krapp et al. 2012;Krapp 2013) were used for genotyping E. magalhaesii specimens following the PCR assay described by Krapp et al. (2012). Electrophoresis on high-resolution PAA gels was conducted in the same way as described above for nSSRs. ...
... Four chloroplast microsatellite markers (hereafter "cpSSRs") originally developed for Dyckia marnier-lapostollei var. estevesii (Krapp et al. 2012;Krapp 2013) were used for genotyping E. magalhaesii specimens following the PCR assay described by Krapp et al. (2012). Electrophoresis on high-resolution PAA gels was conducted in the same way as described above for nSSRs. ...
Article
Encholirium is a genus of 31 xerophytic terrestrial or epilithic bromeliad species endemic to eastern Brazil. Together with Dyckia and Deuterocohnia, it forms the so-called xeric clade of the Pitcairnioideae subfamily of Bromeliaceae. Encholirium species are adapted to rocky landscapes, and many of them are found in the rocky grassland fields of the Espinhaço in the state of Minas Gerais, which is considered the diversity center of the genus. Encholirium species and other bromeliads growing on isolated, island-like habitats like rock outcrops and “inselbergs” are often characterized by high levels of genetic structure and limited gene flow among populations, but there are also exceptions. In the present study, we applied nuclear and chloroplast microsatellite markers to investigate the genetic diversity and population structure of E. magalhaesii L.B.Sm., an endemic species of the Espinhaço, collected in four localities of the Diamantina municipality in southeastern Brazil. Moderate genetic differentiation among localities was revealed by the nuclear markers (Fst = 0.199), whereas genetic structuring was much higher with plastid markers (Fst = 0.496). Estimations of pollen/seed flow ratios suggest that pollen flow is more efficient in maintaining the genetic connectivity among E. magalhaesii populations than seed flow.
... The primers used were DSSR-N01, DSSR-L01, DSSR-N16 and DSSR-N05. PCRs were performed according to the protocol described by Krapp et al. (2012). Genotyping was performed using the same procedure as for nuclear microsatellite markers. ...
Article
The movement of organisms or genes among resource patches is fundamental to the persistence of natural populations over time. Species occurring in rock outcrops may have difficulty maintaining genetic connectivity due to the natural disjunct distribution of these formations, which may lead to genetic differentiation. In this study, we tested the hypothesis of genetic isolation among populations of Deuterocohnia meziana on rock outcrops in Brazil. We evaluated genetic diversity and structure, number of migrants, and the contribution of pollen and seed to dispersal. Additionally, we used niche modelling to estimate the potential distribution of D. meziana and combined this with genetic data to identify potential dispersal routes under different climatic scenarios from the Quaternary. Deuterocohnia meziana showed high diversity and moderate genetic structure, low number of migrants and more efficient dispersal by pollen. Only populations separated by > 70 km showed genetic differentiation. Dispersal routes varied mainly in the intensity of the environmental suitability and indicated the present scenario as the most favourable for gene flow in D. meziana. Our findings contribute to the understanding of processes related to the connectivity and isolation of naturally fragmented populations, highlighting the role of biotic and abiotic drivers for genetic differentiation.
... Bromelioideae and man-made hybridisations as well as natural hybrids are well known (FCBS Bromeliad Natural Hybrids Online Database; FCBS Bigenerics database). Furthermore, molecular studies indicated a problematic delimitation of species within Bromeliaceae (Dyckia:Krapp et al., 2012; Pitcairnia: Palma-Silva et al., 2011; Puya: Schulte et al., 2010) and the reproductive barriers ...
Thesis
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Phylogenetic trouble unleashed The first part of my thesis deals with a comprehensive phylogeny of the Bromelioideae subfamily. The family Bromeliaceae is subdivided into eight subfamilies, one of them is the Bromelioideae. Phylogenetic relationships among the Bromelioideae are still poorly understood and many of the extant genera are suspected to be not monophyletic. Especially Aechmea, the largest and most polymorphic genus constitutes many questions and the genus was used as a depot for taxonomically problematic species. The phylogenetic study presented here is the most comprehensive one so far, covering about half of the known species (434 of 965, Table 1) of Bromelioideae. The phylogeny was generated using plastid (atpB-rbcL, matK, rps16, ycf1_1, ycf1_6) and nuclear (AGT1_exon, ETS, G3PDH, PHYC, RPB2) genetic markers. The markers were analysed individually as well as combined using maximum likelihood and Bayesian analysis. The comparison of plastid vs. nuclear data revealed significant differences which were discussed in detail and hypothesised to indicate hybridisation in certain lineages. Nevertheless, the combination of both datasets increased the overall resolution of the phylogeny and was used to discuss the results in the light of previous studies. The entire phylogeny was divided into 32 groups for discussion. These groups represent potential genera or starting points for further studies in order to reorganise the polyphyletic genera of Bromelioideae into monophyletic lineages. Many extant genera of the eu-Bromelioideae were found to be not monophyletic. Monophyly was observed for the genera Acanthostachys, Billbergia, Cryptanthus, Disteganthus, Hoplocrypanthus, Lapanthus, Orthocryptanthus, Orthophytum, Rokautskyia, Ronnbergia, Sincoraea, Wittmackia and the monotypic ones (Deinacanthon, Eduandrea, Fascicularia, Hohenbergiopsis, Pseudananas). The genus concept proposed by Smith and Downs (1979) is therefore rejected, as well as the taxonomic utility of petal appendages, which were mainly used to delimit genera. In summary, this study and recent studies highlighted other morphological characters (e.g. pollen morphology, stigma type) as much more informative. However, no single character should be used to delimit genera and combinations of relevant characters are required. Even the petal appendages can pose a taxonomical important character at certain taxonomic level. The combination of biogeography and phylogeny revealed that species of some groups which co- occur in a biome or region are also phylogenetically closely related. These groups were not recognised before because the misinterpretation of homoplastic characters led to wrong taxonomical conclusion. For example, the recent re-organisation of the Cryptanthoid group and the re-establishment of Wittmackia with the former Hohenbergia subgen. Wittmackiopsis species highlighted, among other characters, the importance of biogeography. Another case is the subgenus Neoregelia subgen. Hylaeaicum which is geographically and phylogenetically separated from the Nidularioid group and therefore has to be excluded. 5 The large phylogeny presented here gives evidence for multiple invasions of the Brazilian biomes (Amazon Forest, Atlantic Forest, Cerrado, Caatinga) as well as of Central America and the Greater Antilles. It is important to note that the phylogeny is lacking resolution in the deeper nodes. Confident assumptions are therefore hindered and the historical biogeography of Bromelioideae remains cryptic. Anyway, the Atlantic Forest is nowadays the diversity hotspot of the core Bromelioideae and critically endangered. Extensive conservation efforts are required to protect the diverse flora, including the bromeliads. The genetic markers used so far in bromeliad phylogenies provided only limited variation resulting in often unresolved complexes. The search for additional suitable genetic markers in bromelioid phylogenies yielded the nuclear marker AGT1. The amplified fragment consists of one well conserved exon region as well as a highly variable intron. The intron was too variable for aligning it across the entire bromelioid set. On the other hand, the intron provides relevant information for inferring phylogenies of closely related species groups (e.g. in Ananas, Cryptanthoid group). Furthermore, AGT1 is proposed as a genetic barcode in Bromelioideae because it poses much more information then the commonly used ones (e.g. matK). Does size matter? The second part of this thesis deals with the genome size evolution within the family Bromeliaceae. Samples from seven subfamilies were screened with the emphasis on the subfamily Bromelioideae. The data were combined with data from literature and the observed patterns were discussed in relation to known phenomena (e.g. correlations to environment and life form). In the second sub-chapter I have chosen the species Tillandsia usneoides to study the intraspecific genome size variation in combination with morphology and biogeography. Genome size and base composition were measured using the flow cytometry technique. Bromeliaceae comprises mostly diploid species with predominantly 50 small chromosomes (2n), small genome sizes (0.59-4.11 pg) and normal GC content (36.46-42.21 %) compared to other families. Polyploidy was observed so far in the subfamilies Bromelioideae, Tillandsioideae and Pitcairnioideae. Triploids, tetraploids and potential hexaploids were identified. The genera show significant differences in holoploid genome size and base composition throughout the entire family. GC content is weakly positively correlated with genome size. Significant intraspecific genome size variation has been observed, including polyploidization, but no endopolyploidy and no variation in dioecious species. Within the subfamily Bromelioideae, the observed genome size between the early diverging lineages and the core Bromelioideae supports this division. The differences are due to a higher proportion of polyploids in the early diverging lineages and a significant higher 6 GC content in the core Bromelioideae. Both groups differ in their life strategies and occupy principally different habitats with corresponding morphological adaptations. Hence, the early diverging lineages are predominantly terrestrial and xeromorphic. In contrast, the prevailing epiphytic core Bromelioideae are characterised by a tank habit and mostly adapted to more humid environments. Across the family and the subfamily Bromelioideae in particular, significant genome size differences between the different life forms have been observed, but no correlation to biomes within Brazil. Tillandsia usneoides is the most widely distributed species of the family Bromeliaceae. It ranges from the southeastern United States to Argentina and Chile. Tillandsia usneoides grows epiphytic and is dispersed by seeds as well as by fragments of the plant. Within the species striking morphological differences can be observed as far as size characters are concerned. Morphotypes have shown to be stable in cultivation while growing under the same conditions. In order to investigate possible reasons for the variation the relative genome size of 75 specimens covering the whole distribution range was measured and combined with morphological, distribution and climatic data. Significant variation in the relative genome size corresponded to the morphological differences and reflected the north-south distribution gradient. Genome size and morphotypes showed a positive correlation, as well as with the mean temperature of the driest and coldest quarter and the minimal temperature of the coldest month.
... Four chloroplast microsatellite markers (hereafter cpSSRs; see online Appendix S2 for locus characteristics) originally developed for Dyckia marnier-lapostollei var. estevesii by Krapp et al. (2013) and Krapp (2013) were used to genotype E. spectabile specimens following the PCR assay described by Krapp et al. (2012) . Electrophoresis in high-resolution PAA gels was conducted in the same way as described above for nSSRs. ...
Article
Premise of the study: Inselbergs are terrestrial, island-like rock outcrop environments that present a highly adapted flora. The epilithic bromeliad Encholirium spectabile is a dominant species on inselbergs in the Caatinga of northeastern Brazil. We conducted a population genetic analysis to test whether the substantial phenotypic diversity of E. spectabile could be explained by limited gene flow among populations and to assess the relative impact of pollen vs. seed dispersal on the genetic structure of the species. Methods: Nuclear and chloroplast microsatellite markers were used to genotype E. spectabile individuals from 20 rock outcrop locations, representing four geographic regions: northern Espinhaço Range, Borborema Plateau, southwestern Caatinga and southeastern Caatinga. F-statistics, structure, and other tools were applied to evaluate the genetic makeup of populations. Key results: Considerable levels of genetic diversity were revealed. Genetic structuring among populations was stronger on the plastid as compared with the nuclear level, indicating higher gene flow via bat pollination as compared with seed dispersal by wind. structure and AMOVA analyses of the nuclear data suggested a high genetic differentiation between two groups, one containing all populations from the southeastern Caatinga and the other one comprising all remaining samples. Conclusions: The strong genetic differentiation between southeastern Caatinga and the remaining regions may indicate the occurrence of a cryptic species in E. spectabile. The unique genetic composition of each inselberg population suggests in situ conservation as the most appropriate protection measure for this plant lineage.
Article
In the Atlantic Rainforest located north of the São Francisco River (northeast Brazil), the humid enclaves called brejos de altitude play a significant role in the diversity dynamics of local flora and fauna. The related species Dyckia pernambucana and D. limae (Bromeliaceae) are characterized by their narrow endemic occurrence in such brejos, and their species status remains unclear. In order to understand the species delimitation in those assigned taxonomic entities, patterns of gene flow and genetic variability were calculated using nuclear and plastid microsatellites and AFLP markers. In this regard, we collected populations of the Pernambuco complex (D. limae and D. pernambucana, from the Borborema Plateau) and the closest relative D. dissitiflora (from the northern Espinhaço Range). Genetic diversity was moderate, despite the possible influence of genetic drift and selfing rates. Dyckia limae could not be undoubtedly discriminated from the remaining populations of Pernambuco, and we propose the synonymization of these species. Thus, the conservation of D. limae as a formerly single species would not reflect the conservation of the minimal gene pool of the studied lineage (D. pernambucana). We also propose the revalidation of the conservation status of this species, endemic to anthropomorphic island-like mountains environments. Finally, the associations found here were consistent with the historical patterns of colonization and fragmentation of the Atlantic Rainforest.
Article
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Genetic diversity and population structure in plants are directly associated with the reproductive system and gene flow by pollen and seeds. We examined the reproductive system, pollination biology, genetic diversity and structure, and gene flow in Bromelia hieronymi, an endemic species of the humid Brazilian chaco. We characterized the reproductive system by hand-pollination experiments and the pollination biology by observations, both in situ. For the genetic analysis we used nuclear and plastid microsatellite markers. Bromelia hieronymi is allogamous, self-incompatible and clonal. The potential pollinators were hawkmoths and hummingbirds, but butterflies were also observed. The three populations studied showed high levels of genetic diversity for nuclear (mean observed and expected heterozygosity HO = 0.624 and HE = 0.558) and plastid markers (mean HE = 0.688) and moderate genetic structure (fixation index FST = 0.138); we found evidence of genetic bottlenecks in two populations. The selfincompatibility system may have a strong relationship with gene flow, and its association with clonality may be responsible for the high genetic diversity observed. Gene flow by seeds was more efficient than gene flow by pollen. These results show that B. hieronymi responds negatively to reduction in population size. Therefore, continuous conservation strategies are necessary to avoid increasing genetic differentiation in the species, maintaining its evolutionary potential for adaptation.
Article
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We applied a series of intra- and interspecific in situ cross-pollination experiments under greenhouse conditions to evaluate the breeding systems in four Fosterella species (Pitcairnioideae s.str.; Bromeliaceae). Viable hybrids were produced between each pair of the investigated species, suggesting that reproduction barriers may be low also under natural conditions. Seed germination rates proved to be high in each crossing treatment, indicating a high viability of the artificial hybrids. Large numbers of seeds were produced after both closed and open pollination treatments, suggesting that autogamy may be a major reproductive strategy in the genus. Our results support the concept that self-compatibility is an appropriate way to avoid natural hybridization in Bromeliaceae and could assist in maintaining species integrity in the presence of pollen flow. Paternity was verified in all crosses by genotyping parents and offspring with a set of polymorphic nuclear microsatellite markers. To study the mode of chloroplast inheritance, we developed a novel set of 24 chloroplast microsatellite markers using 454 pyrosequencing technology, and applied four of these markers for genotyping parents and offspring from all crosses. Our results clearly demonstrated a maternal inheritance of plastids.
Article
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Premise of the study: Polymorphic microsatellite markers were developed for Fosterella rusbyi (Bromeliaceae) to evaluate the population genetic structure and genetic diversity of natural populations of F. rusbyi and other Fosterella species in Bolivia. Methods and results: 454 pyrosequencing technology was used to generate 73027 sequence reads from F. rusbyi DNA, which together contained 2796 perfect simple sequence repeats (SSRs). Primer pairs were designed for 30 loci, of which 15 were used to genotype 30 F. rusbyi plants from two geographical areas in Bolivia. All markers were polymorphic, with two to nine alleles in the overall sample. Cross-species amplification was tested in 10 additional Fosterella species. Seven loci showed consistent amplification in six or more species. Conclusions: The 15 SSR markers developed for F. rusbyi are promising candidates for population genetic analyses within F. rusbyi and other species of Fosterella.
Article
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Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes. Electronic supplementary material The online version of this article (doi:10.1007/s00239-009-9317-3) contains supplementary material, which is available to authorized users.
Article
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A poor man's approach to genotyping for research and high-throughput diagnostics.
Article
The genus Dyckia (Bromeliaceae) comprises 147 species that are distributed in Brazil and adjacent countries. Many species are rare and narrow endemics. We used 454 pyrosequencing to isolate 1,587 microsatellite loci in Dyckia marnier-lapostollei. Of 50 loci that were selected for primer design, 15 markers proved to be polymorphic in five populations from three heterologous species, Dyckia dissitiflora, Dyckia pernambucana and Dyckia limae. Numbers of alleles per locus varied from 3 to 30, and expected and observed heterozygosities ranged from 0.21 to 0.53 and from 0.16 to 0.44, respectively, in the overall sample. The 15 new microsatellite markers are promising tools for studying population genetics in Dyckia species.
Article
We present a simple protocol for DNA isolation from climbing cacti, genera Hylocereus and Selenicereus. The abundant polysaccharides present in Hylocereus and Selenicereus species interfere with DNA isolation, and DNA extracts, rich in polysaccharides, are poor templates for amplification using polymerase chain reaction (PCR). We used roots as the source tissue due to the lower viscosity of the extracts relative to that of other tissues. The extraction and isolation procedure we devised consists of the following steps: (1) three washes of ground tissue with the extraction buffer to remove the polysaccharides; (2) extraction with high-salt (4 M NaCl) cetyltrimethylammonium bromide (CTAB) buffer to remove the remaining polysaccharides; (3) removal of RNA by RNase; (4) phenol:chloroform extraction to remove proteins; (5) chloroform extraction to remove remaining phenols. The yields ranged from 10 to 20 g DNA/g fresh roots. DNA samples prepared by our method were consistently amplifiable in the RAPD reaction and gave reproducible profiles.
Article
Chloroplast microsatellites, or simple sequence repeats (cpSSRs), are typically mononucleotide tandem repeats. When located in the noncoding regions of the chloroplast genome (cpDNA), they commonly show intraspecific variation in repeat number. Despite the growing number of studies applying cpSSRs, studies of economically important plants and their relatives remain over-represented. Thus, the potential of cpSSRs to offer unique insights into ecological and evolutionary processes in wild plant species has yet to be fully realized. This review provides an overview of the technical resources available to aid cpSSR discovery including a list of cpSSR primer sets available and cpDNA sequencing resources. Our updated analysis of 99 whole chloroplast genomes downloaded from GenBank confirms that potentially variable cpSSRs are abundant in the noncoding cpDNA of plants. Overall variation in the frequency of cpSSRs was extreme, ranging from one to 700 per genome (median = 93), while in 81 vascular plants, between 35 and 160 cpSSRs were detected per genome (median = 86). We offer five recommendations to aid wider development and application of cpSSRs: (i) When genus-specific cpSSR primers are available, cross-species amplification can often be fruitful. (ii) While potentially useful, universal cpSSR primers at best provide access to only a small number of variable markers. (iii) De novo sequencing of noncoding cpDNA is the most effective and efficient way to develop cpSSR markers in wild species. (iv) DNA sequencing of cpSSR alleles is essential, given the complex nature of the genetic variation associated with hypervariable cpDNA regions. (v) The reliability of cpSSR length based genetic assays need to be validated in all studies.
Till 6020 (WU) Cerros Acahay, Paraguari (PY) −25.9167
  • Dyckia
  • W Baker
Dyckia microcalyx Baker W. Till 6020 (WU) Cerros Acahay, Paraguari (PY) −25.9167; −57.1500
PhyDE: Phylogenetic data editor. Version 0.9971. Program distributed by the author
  • J K Müller
  • Müller
  • Quandt
MÜLLER, J., K. MÜLLER, AND D. QUANDT. 2010. PhyDE: Phylogenetic data editor. Version 0.9971. Program distributed by the author. Website http://www.phyde.de/ [accessed 23 November 2010].
Schindhelm s.n. (HD) Pedra Azul, Minas Gerais (BR) −15.9867
  • L B Encholirium Horridum
  • W Sm
Encholirium horridum L. B. Sm. W. Schindhelm s.n. (HD) Pedra Azul, Minas Gerais (BR) −15.9867; −41.4069