Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba

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Highly'accelerated'rates'of'genomic'rearrangements'and'nucleotide'
substitutions'in'plastid'genomes'of'Passiflora'subgenus'Decaloba!
Bikash Shresthaa,, Mao-Lun Wengb, Edward C. Theriota, Lawrence E. Gilberta, Tracey A. Ruhlmana, Shawn E. Krosnickc, Robert K. Jansena
aDepartment of Integrative Biology, University of Texas at Austin, Austin, TX, USA; bDepartment of Biology, Westfield State University, Westfield, MA, USA; cDepartment of Biology, Tennessee Tech University, Cookeville, TN, USA
Passiflora
is included among a small group of angiosperm taxa with
highly rearranged plastid genomes (plastomes) that exhibit a syndrome
of features, including biparental inheritance and plastome-genome
incompatibility. However, plastid genomic studies in
Passiflora
are
limited in taxon sampling and confined mainly to the largest subgenus
Passiflora
. To examine phylogenetic extent of plastome rearrangements
in Passifloraceae, 16 new plastomes of species across all five
subgenera and an outgroup
Adenia
were completed. With these newly
completely plastomes along with previously published
Passiflora
plastomes, this study addresses four major questions:
i) Does expanded taxon sampling of plastomes resolve the
incongruence with previously published phylogenies?
ii) Which protein coding genes provide the most phylogenetic
signal?
iii) What is the extent of genomic rearrangement and its
phylogenetic distribution?
iv) What are the patterns of nucleotide substitutions in protein
coding genes?
Introduction
Species
ycf1*
trnN
trnR+
rrn5
rrn4.5
rrn23
trnA
trnI
rrn16
trnV
rps12-3'
rps7
ndhB
trnL
ycf2
trnI
rpl23
rpl2
rps19*
Populus ycf1* + + + + + + + + + + + + + + + + + + rpl22*
A.)mannii + + + + + + + + + + + + + + + + + + +
P.)pittieri rps15 + + + + + + + + + + + + + + + + rpl23* - -
P.)arbelaezii rps15 + + + + + + + + + + + + + + + + + + +
P.)foetida + + + + + + + + + + + + + + + + + + +
P.)menispermifolia - - - - - - - - - - + + + +
ycf2Ψ+ + + +
P.)actinia)+)10)others
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + +
P.)contracta + + + + + + + + + + + + + + + + psbA trnI
rpl23*
P.)tetrandra + + + + + + + + + + + + + + + + - - -
P.)microstipula + + + + + + + + + + + + + + + + + + +
P.)obovata - - - - - - - - - - + + + + + + + +
P.)auriculata ndhF*
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD petB psbH psbN psbT psbB clpP rps12-5' atpB atpE trnM trnV rbcL accD psaI ycf4 cemA petA
P.)jatunsachensis/rufa ndhF*
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD petB psbH psbN psbT psbB clpP rps12-5' atpB atpE trnM trnV rbcL accD
P.)tenuiloba
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoAΨpetD petB psbH psbN psbT psbB clpP rps12-5' atpB atpE trnM trnV rbcL accD psaI
P.suberosa ndhF*
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoAΨpetD petB psbH psbN psbT psbB clpP rps12-5' atpB atpE trnM trnV rbcL accD psaI
P.)lutea ndhF*
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD petB psbH psbN psbT psbB clpP rps12-5' atpB atpE trnM trnV rbcL accD psaI ycf4 cemA*
P.filipes ndhF*
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD*
P.)affinis rps15
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD*
P.)biflora
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA petD*
P.misera
ycf1Ψ+ + + + + + + + + + + + + ycf2Ψ+ + + + rps3 rpl16 rpl14 rps8 rpl36 rps11 rpoA
0.02
P. filipes
P. edulis
Populus
P. actinia
P. lutea
P. oerstedii
P. foetida
P. tenuiloba
P. auriculata _S
P. cincinnata
P. cirrhifolia
P. contracta
P. arbelaezii
P. microstipula
P. menispermifolia
P. nitida
P. jatusachensis
P. laurifolia
P. serratodigitata
P. retipetala
P. vitifolia
A. mannii
P. suberosa
P. serratifolia
P. misera
P. biflora
P. rufa
P. tetrandra
P. obovata
P. quadrangularis
P. affinis
P. ligularis
P. auriculata_FG
P. pittieri
9 4
9 7
9 9
3 3
9 3
4 4
9 9
9 8
e,A
a
a, j
a, c, Y, L
b, h
c, Z
c, X
c, E, K
c
c
d
f, i , j, C
f
g, F
c, B
k, D, K
Gene loss
a. rpl20
b. rpl22
c. rpl32
d. rps7
e. rps16
f. ycf1/ycf2
g. rpoA
1, 8-9
9, 13-14
3-6
11-13
16
11-13
10-12
5
Intron loss
h. atpF
i. rpoC1
j. clpP
k. rpl16
D
J
IR expansion
A. JLB – rps19
B. rps19 – rpl22*
C. JLB – rpoA
D. rpoA – petD*
E. petD* – accD
F. petD* – psaI
G. petD* – cemA*
H. accD – petA
I. JSA – ycf1
J. JSA – rps15
K. JSB – ndhF*
L. JLA – psbA
IR contraction
X. JSA – rps12-3’
Y. J LB – trnI
Z. JLB – rpl23*
Gene blocks
1. psbA – trnH-GUG
2. trnK-UUU – psbI
3. trnS-GCU – trnR-UCU
4. atpA – atpH
5. atpI – rpoB
6. trnC-GCA – ycf3
7. rps4 – ndhC
8. trnM-CAU – trnV-UAC
9. atpB – atpE
10. rbcL
11. psbE – accD
12. rpl20 – petL
13. clpP – rps12-5’
14. psbB – petD
15. rpoA – ycf1
16. ndhF – ndhH
K
H
Y
J
G
NA
6-7, 10-13,
8-9
3-6, 8-9
8-9
4-7, 12
X
A
C
B
Genome sequencing, assembly and annotation
• Plastomes for sixteen Passifloraceae species were sequenced using Illlumina data and assembled
de novo
using Velvet and
annotated with DOGMA/GeSeq and tRNAscan-SE.
Phylogenetic analysis
• Sixty-eight protein-coding plastid genes shared by all
Passiflora
and outgroups,
Adenia
and
Populus,
were used to infer
maximum likelihood (ML) tree using IQ-TREE v1.5.2.
Phylogenetic informativeness
• PhyDesign was used to estimate the phylogenetic informativeness profile for 68 protein-coding plastid genes using a relative-
time ultrametric tree.
Nucleotide substitution rate analyses
• Pairwise estimation: Pairwise synonymous (
dS
) and non-synonymous (
dN
) substitution rates were calculated between the
outgroup
Populus trichocarpa
and all other species using PAML.
• Lineage-specific rate analysis: Test for significantly different substitution rates (
dN
and
dS
) and
dN/dS
on the branch leading to
IR expansion within subgenus
Decaloba
, branch models were used in HyPhy and PAML.
Methods
Figure. 1. Distribution of
Passiflora
plastome rearrangements on maximum likelihood tree. Horizontal bar indicates the expected number substitutions per site. Pseudogenes are indicated by
(Ψ ). Species names are color-coded to indicate their generic or subgeneric placement: Red (
Adenia
), cyan (
Astrophea
), orange (
Deidamioides
)
,
blue (
Passiflora
), purple
(
Tetrapathea
), and
green (
Decaloba
).
Results
• Expanded taxon sampling generated trees congruent
with previously published phylogenies (Fig. 1A)
.
• Ten most phylogenetic informative genes (Fig. 2)
generated a tree congruent with the tree using 68
plastid genes.
• Extensive plastome rearrangements were found within
the genus, specifically subgenus
Decaloba
, some of
which occurred multiple times (Fig. 1A-C).
• Gene-specific rate heterogeneity was found for
clpP
and
ribosomal subunits genes primarily in subgenus
Decaloba
(Fig. 3)
.
Figure 3. Boxplot showing the variation in pairwise
dS
and
dN,
and
dN
/
dS
for the
Adenia
+
Passiflora
species Outliers for
each category were labeled with gene names. Clades (A-E) used to group species to calculate statistical significance are
labeled on right-hand side.
Conclusions
Acknowledgements
00.0050.010.0150.020.0250.030.035
1012299.4
2024598.8
3036898.2
4049197.6
5061497
6073796.4
7086095.8
8098395.2
9110694.6
atpAccsAmatK ndhDndhF rbcLrpoB rpoC1rpoC2 ycf4
clpP%
Figure 2. Net phylogenetic informativeness profile for 68 plastid
genes. Ten genes with the greatest informativeness are color-coded.
Read more here!
P. gabrielleana
P. microstipula
dS
dN
dN/dS
0.0 0.2 0.4 0.6 0.8 0.0 0.2 0.4 0.6 0.0 0.5 1.0 1.5
A.mannii
P.arbelaezii
P.pittieri
P.actinia
P.cincinnata
P.edulis
P.foetida
P.laurifolia
P.ligularis
P.menispermifolia
P.nitida
P.oerstedii
P.quadrangularis
P.retipetala
P.serratifolia
P.serratodigitata
P.vitifolia
P.cirrhifolia
P.contracta
P.tetrandra
P.affinis
P.auriculata(FG)
P.auriculata(S)
P.biflora
P.filipes
P.jatunsachensis
P.lutea
P.microstipula
P.misera
P.obovata
P.rufa
P.suberosa
P.tenuiloba
Subgenus
Adenia
Astrophea
Decaloba
Deidamioides
Passiflora
Tetrapathea
A
B
C
D
E
psaC/
psaI/
petL/
petL/
psbI/
rps8/
ycf4/
ycf4/
clpP/
clpP/
clpP/
clpP/
ycf4/
ycf4/
clpP/rpl23/
rpl23/
clpP/
rpl23/
ycf4/
ycf4/
clpP/
clpP/
clpP/
rpl23/
clpP/
clpP/
clpP/rpl36/
rps12/
rps12/
clpP/
ycf4/
clpP/
clpP/
ycf4/
rpl36/
clpP/
clpP/
clpP/
clpP/rpl36/
clpP/