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Sequence characteristics ofthe ITSl, ITS2, and total ITS (ITSl and ITS2) region, and the matK gene in species of Podolepis and related genera
Source publication
The generic circumscription and intra-generic relationships of the genus
Podolepis Labill., with various chromosome numbers from
n = 12 to n = 3,
were examined by sequences of the internal transcribed spacers (ITS) of
nuclear ribosomal DNA and the matK gene of chloroplast
DNA. The topology of the ITS tree for 17 species and the matK tree for 18
spe...
Contexts in source publication
Context 1
... main characteristics of the ITSl, ITS2, total ITS (ITSI and ITS2) region, and the matK gene are listed in Table 3. The length ofITS 1 varied from 251 bp (in Leptorhynchos medius and Triptilodiscus pygmaeus) to 259 bp (in Chrysocephalum apiculatum) and 19 sites of in de Is were found among the 30 taxa examined. ...
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Citations
... Anderberg (1991) agreed that, based on general morphology, floret morphology and other features, Podolepis was probably polyphyletic. A study based on molecular systematics (Konishi et al. 2000) would also suggest that Panaetia and Siemssenia are sister to Podolepis and could be recognised at some level. ...
... Podolepis kendallii is an unusual member of the Gnaphalieae by virtue of its distinctive fruit (longpapillose) and pappus (bristles distinctly plumose at the apex) morphology (Konishi et a/. 2000). The various consensus trees derived by Konishi et al. (2000) show P. kendallii grouping with Waitzia J.C.Wendl., which otherwise has "..little similarity in fruit morphology and other morphological characteristics" (Konishi et. al. 2000). Other authors (e.g. Short et al. 1989 commented about the uniqueness of P. kendallii and suggested ...
... 2000). The various consensus trees derived by Konishi et al. (2000) show P. kendallii grouping with Waitzia J.C.Wendl., which otherwise has "..little similarity in fruit morphology and other morphological characteristics" (Konishi et. al. 2000). ...
... Stebbins [115,116] provides evidence that there are patterns, although they are not universal. In some genera, increasing specialization has been achieved by reduction in genome size with a shift from perennial to annual growth habit or a shorter growing season, such as: Crepis [35], Artemisia [66], Lathyrus [46,85], Papaver [49], Asphodelus [14], Allium [71], Helianthus [105], Ranunculus [108], Podolepis [38], Arachis [106]. Conversely, increasing genome size ostensibly has accompanied the shift to the annual habit or shorter growing season in Lolium [86], Anthemis and Anacyclus [66]. ...
... Conversely, increasing genome size ostensibly has accompanied the shift to the annual habit or shorter growing season in Lolium [86], Anthemis and Anacyclus [66]. In some genera, ecological shifts also have been associated with changes in chromosome number, e.g. the shift from perennial to annual habit in arid land races appears to have been accompanied by reduction in chromosome number in Calotis [111,112], Podolepis [38], for further details, see Levin [51]. ...
Karyotype characterizing the phenotypic aspects of the chromosome complement represents structural and functional organization of the nuclear genome. Its constancy ensures transfer of the same genetic material to the next generation, while variation enables ecological differentiation and adaptation. Superimposition of karyotype information onto a phylogenetic framework has immense utility in elucidating direction of evolutionary change and delineation of taxonomic hierarchy. This article attempts to provide an illustrated description of the chromosomal features that are useful in discerning differences and affinities between species and taxa. A detailed account of experimental parameters useful in chromosome identification and evaluation of karyotype asymmetry is furnished citing suitable examples. In addition to various karyotypic indices, special emphasis is given to the quantitative parameter of “chromosome dispersion index (DI)” that promises phylogenetic differentiation of closely related karyotypes, since most genera of herbaceous angiosperms display interspecific differences in chromosome size and symmetry, if not number. Karyo-evolutionary trends involve both change in chromosome number, morphology/karyotype symmetry, ploidy and total haploid length. The pattern of DNA addition/deletion across the chromosome complement has been found to be variable. Such change in DNA is either equally shared by all the chromosomes or is proportionately shared commensurate to chromosome size, leading to differential pace of change in karyotype asymmetry across the taxa. The large data accumulating on chromosome number over the years offer opportunities to utilize them as additional tools in taxonomy. The basic chromosome number (ancestral haploid number) in angiosperms has been suggested as n = 7, and an ancestral 1C of 1.73 pg, which is characteristic of the major groups with slight deviation in certain orders. The average ‘holoploid genome size’ i.e. 1C, for the Angiosperms is inferred to be 5870 Mb/6.0 pg. However, the 1C-value data available for ca.10800 species of Angiosperms reveal genome size diversity ranging from 61 Mb/0.0648 pg in the carnivorous plant Genlisea tuberosa (Lentibulariaceae) to 1,49,000 Mb/152.23 pg in Paris japonica (Melanthiaceae) suggesting over 2400 fold variation across the angiosperms; and 230 fold variation within the family (0.66 pg in Schoenocaulon texanum vs. P. japonica with highest C value). Metaphase chromosome size is estimated to range from the shortest ~ 0.3 µm in Genlisea aurea, and at family level from ~ 0.8 µm in Chamaelirium luteum to ~ 30 µm in Paris japonica. Chromosome number ranges from n = 2 to 320 across the angiosperms, at family level from n = 4 to 120 in the Brassicaceae, and at genus level from n = 2 to 45 in Brachyscome (Compositae).The evolution has mostly been at the diploid level. It is generally believed that the chromosome size of monocots is larger than dicots and the chromosome size of temperate plants is larger than tropical plants. For a broader sense and larger scale understanding, the evolutional conception of karyotype is principally based on the thoughts that: (i) symmetrical karyotype is more primitive than asymmetrical ones, (ii) longer chromosomes are primitive than shorter ones, (iii) median centromeres with chromosome arms of equal length are more primitive than chromosome arms of unequal length, (iv) low basic numbers had given rise to higher ones, and the taxa with variable chromosome number are considered young and still in evolutionary flux, (v) species with one NOR site per haploid genome are considered advanced than multiple NOR sites, (vi) ancient species had less heterochromatin (repetitive DNA), the primitive species accredited heterochromatin, followed by gradual shedding of excess heterochromatin with evolutionary specialization.However, discovery of ancient episodes of Whole Genome Duplication (WGD) events said to have happened as an escape to the 5th mass extinction at the end of Cretaceous as a survival strategy has opened newer possibilities. A new thinking is beginning to emerge that concomitant with the climate change happening at a fast pace in the Anthropocene, it is likely that if global climate undergoes major change in coming centuries then auto-polyploidization could be the important player leading to increase in chromosome number.
... Although it is to be expected that dysploidy will operate as a step-bystep process (Murray, 2002;Guerra, 2012), when a phylogenetic framework is included in cytogenetic studies drastic reductions in chromosome numbers have been detected in lineages of Podolepis Labill. and Brachyscome Cass., both members of Asteraceae ( Watanabe et al., 1999;Konishi, Watanabe & Kosuge, 2000). For instance, B. dichromosomatica C.R.Carter, with a chromosome number of n = 2, belongs to a clade the ancestors of which probably had n = 9 (Watanabe et al., 1999); on the other hand, P. capillaris (Steetz) Diels, with n = 3, has a sister species (P. ...
... For instance, B. dichromosomatica C.R.Carter, with a chromosome number of n = 2, belongs to a clade the ancestors of which probably had n = 9 (Watanabe et al., 1999); on the other hand, P. capillaris (Steetz) Diels, with n = 3, has a sister species (P. microcephala Benth.) with n = 11, the ancestor of which probably had n = 12 ( Konishi et al., 2000). There is some evidence for an association between chromosome number, genome size and the shift from perennial to annual habitat, especially in plants thriving in stressful environments ( Watanabe et al., 1999;Levin 2002;Carta, Bedini & Peruzzi, 2018). ...
... Helianthemum represents an excellent case study for disentangling chromosome number evolution since, at least with available data, the short-lived ecological specialist shrub H. squamatum is the only member of this genus with the lowest chromosome number and, contrary to previously knowledge, belongs to a recent evolutionary lineage. In this study, we combine data on chromosome numbers and nuclear DNA content (see Guerra, 2012) in a comprehensive phylogenetic framework that allows us to assess the hypothesis that a large-scale genome reorganization yielding a drastic reduction in the chromosome number took place in this lineage in parallel with its ecological specialization (Stace, 1978;Watanabe et al., 1999;Konishi et al., 2000;Carta et al., 2018). To achieve this we: (1) modelled the evolution of chromosome number in Helianthemum to gauge rates of gains or losses of chromosomes, polyploidization or other models of chromosome number variation in the lineages; (2) analysed the karyotype and the nuclear DNA content of H. squamatum and its sister species H. syriacum and (3) studied the meiotic process in pollen mother cells (PMCs) in H. squamatum as a means of shedding further light on the genome reorganization presumed to have taken place in this species. ...
Helianthemum squamatum is a specialist gypsophile, the only species of a recently diverged lineage in subgenus Helianthemum characterized by having the lowest chromosome number in the genus (n = 5). With the hypothesis of great genome reorganization in the lineage of H. squamatum, we (1) modelled the evolution of the chromosome number in the genus Helianthemum, (2) analysed the karyotype and the nuclear DNA content of H. squamatum and its sister species H. syriacum (n = 10) and (3) studied in detail the meiotic process of H. squamatum. Our analyses show that: (1) the rate of chromosome losses in the lineage that gave rise to H. squamatum is 100 times higher than in the genus as a whole; (2) compared to its sister species, H. squamatum has a more symmetric karyotype composed of longer metacentric chromosomes and retains c. 80% of its nuclear DNA content and (3) achiasmatic behaviour of chromosomes occurs during microsporogenesis despite full synapsis. Our results are in agreement with previous knowledge showing that reduced chromosome numbers in determinate lineages are found in short-lived species adapted to stressful environments, and we suggest that a combination of fewer chromosomes, a smaller genome, a shorter life cycle and the suppression of meiotic recombination can together contribute to the maintenance of those advantageous allelic combinations that makes H. squamatum a true gypsophile, enabling the individual plants to cope with the harshness imposed by dry gypsum soils.
... This is consistent with previous suggestions of secondary chromosome number reduction in Gnaphalieae (Watanabe et al. 1999) particularly Podolepis Labill. (Konishi et al. 2000), in which n = 12, 11, 10, 9, 8, 7 and 3 were reported. Interspecific polyploidy in the Gnaphalieae has played an important role in the evolution of many genera (Watanabe et al. 1999). ...
Leontopodium R. Br. ex Cass. is the second largest genus within the Asian Gnaphalieae (Asteraceae) and is most diversified on the Qinghai-Tibet Plateau and its adjacent areas of SW China. The chromosome numbers and karyomorphology of five species from this region were investigated for the first time: Leontopodium sinense (2n = 28 = 22m + 6sm), L. muscoides (2n = 24 = 22m + 2sm), L. souliei (2n = 52 = 32m + 20sm), L. pusillum (2n = 72 = 52m + 20sm), and L. nanum (2n = 48 = 24m + 24sm). The results suggest that the basic chromosome number of Leontopodium is x = 14, followed with dysploidy numbers (e.g. x = 12, 13). Polyploidization has also played an important role in the evolution of Leontopodium in this region.
... An ancestral base chromosome number of x = 7 has been proposed for the tribe (Ward & al., 2009), but in each of the focal groups species with 2n = 28 or higher are com- mon, implying an important role for polyploidy in their history ( Galbany-Casals & Romo, 2008;Ward & al., 2009). Lower base numbers also occur among endemic Australian genera (as low as n = 3: see Ward & al., 2009), and in African Heli chrysum (n = 4: Galbany-Casals & Romo, 2008), but at least some of these low numbers are proposed to be the result of secondary reduction ( Konishi & al., 2000;Galbany-Casals & Romo, 2008) ...
... This is consistent with previous suggestions of secondary chromosome number reduction in Australian Gnaphalieae ( Watanabe & al., 1999) particularly Podolepis Labill. ( Konishi & al., 2000), in which n = 12, 11, 10, 9, 8, 7, 3 are reported. ...
Phylogenetic analyses have suggested that the everlasting daisy tribe Gnaphalieae colonized the globe repeatedly and rapidly from southern Africa. However, both the circumscription of monophyletic groups of “out of Africa Gnaphalieae genera and the identification of their sister groups in southern Africa has proved difficult. We have analysed sequences of nrDNA spacers (ITS, ETS), cpDNA (ndhF, trnL intron, trnL-trnF intergenic spacer, trnK intron), and low-copy nuclear markers to examine selected relationships within the crown radiation of the tribe. We focused on relationships among two putative clades suggested by previous studies and a representative sampling of genera endemic to Australasia. Incongruities between nrDNA and cpDNA trees are frequent and some involve robustly supported clades. However, trees generated for two low-copy nuclear markers are largely congruent with each other but imply that allopolyploidy preceded the radiations of at least four separate extant lineages within the tribe, one largely or entirely restricted to Australasia, one almost global, and two still poorly sampled. Collectively, these four putative allopolyploid lineages may account for more than half of the described species diversity of the tribe.
... We also tested possible phylogenetic incongruities, as reported in other phylogenetic studies in Gnaphalieae (Smissen & al., 2004). Combined nuclear and chloroplast phylogenies have been successfully used in Compositae and Gnaphalieae at the generic and species levels (Bayer & al., 2000(Bayer & al., , 2002Konishi & al., 2000;Álvarez & al., 2001;Susanna & al., 2003;Liu & al., 2004;Lee & al., 2005;Sonnante & al., 2007). We gathered information from several datasets of non-coding sequences, including ITS and ETS sequences of nrDNA, together with the ycf3-trnS and trnL introns and trnL-trnF and trnT-trnL spacers of cpDNA. ...
The precise generic delimitation of Aliella and Phagnalon and their tribal affinities are at present unresolved. The main goals of our study were to verify the monophyly of these two genera and to determine their closest affinity group within Gnaphalieae. We analysed sequences of the trnL intron and trnL-trnF spacer of Gnaphalieae and other Compositae tribes, in order to elucidate the tribal position of Aliella, Macowania, Phagnalon and Philyrophyllum. In addition, we analysed ribosomal nrDNA together with the ycf3-trnS and trnT-trnL spacers of cpDNA to elucidate the relationships within Aliella and Phagnalon. The genera Anisothrix, Athrixia and Pentatrichia are closely related to Aliella and Phagnalon. Aliella, Macowania and Phagnalon are nested within the "Relhania clade", and the subtribal affinities of Philyrophyllum lie within the "crown radiation clade". The monophyly of Aliella and Phagnalon is not supported statistically and Aliella is paraphylethic in most of the analyses. The resulting phylogeny suggests an African origin for Aliella and Phagnalon and identifies three main clades in Phagnalon, the Irano-Turanian clade, the Mediterranean-Macaronesian clade and the Yemenite-Ethiopian clade. Some endemics to Yemen and Ethiopia are resolved in the Mediterranean-Macaronesian clade, providing new evidence of phytogeographical links between Macaronesia, Eastern Africa and Southern Arabia. Incongruence between the chloroplast and nuclear molecular data and the lack of resolution in some clades may indicate that hybridization could have played an important role in the evolution and diversification of Phagnalon and Aliella.
... We also tested possible phylogenetic incongruities, as reported in other phylogenetic studies in Gnaphalieae (Smissen & al., 2004). Combined nuclear and chloroplast phylogenies have been successfully used in Compositae and Gnaphalieae at the generic and species levels (Bayer & al., 2000(Bayer & al., , 2002Konishi & al., 2000;Álvarez & al., 2001;Susanna & al., 2003;Liu & al., 2004;Lee & al., 2005;Sonnante & al., 2007). We gathered information from several datasets of non-coding sequences, including ITS and ETS sequences of nrDNA, together with the ycf3-trnS and trnL introns and trnL-trnF and trnT-trnL spacers of cpDNA. ...
The precise generic delimitation of Aliella and Phagnalon and their tribal affinities are at present unresolved. The main goals of our study were to verify the monophyly of these two genera and to determine their closest affinity group within Gnaphalieae. We analysed sequences of the trnL intron and trnL‐trnF spacer of Gnaphalieae and other Compositae tribes, in order to elucidate the tribal position of Aliella, Macowania, Phagnalon and Philyrophyllum. In addition, we analysed ribosomal nrDNA together with the ycf3‐trnS and trnT‐trnL spacers of cpDNA to elucidate the relationships within Aliella and Phagnalon. The genera Anisothrix, Athrixia and Pentatrichia are closely related to Aliella and Phagnalon. Aliella, Macowania and Phagnalon are nested within the "Relhania clade", and the subtribal affinities of Philyrophyllum lie within the "crown radiation clade". The monophyly of Aliella and Phagnalon is not supported statistically and Aliella is paraphylethic in most of the analyses. The resulting phylogeny suggests an African origin for Aliella and Phagnalon and identifies three main clades in Phagnalon, the Irano‐Turanian clade, the Mediterranean‐Macaronesian clade and the Yemenite‐Ethiopian clade. Some endemics to Yemen and Ethiopia are resolved in the Mediterranean‐Macaronesian clade, providing new evidence of phytogeographical links between Macaronesia, Eastern Africa and Southern Arabia. Incongruence between the chloroplast and nuclear molecular data and the lack of resolution in some clades may indicate that hybridization could have played an important role in the evolution and diversification of Phagnalon and Aliella.
... Phylogenetic studies using DNA sequencing data are becoming routine in plant systematics (Konishi et al. 2000;Wright et al. 2000;Neyland 2002;Petersen et al. 2002;Steane et al. 2002;Murphy et al. 2003; also see Small et al. 2004 for review;Shepherd et al. 2005). Such studies are independent of environmental influences on phenotypic characters and developmental stages that can affect morphological characters. ...
A complete botanical key for the genus Ptilotus R. Brown ( family Amarathaceae) has not yet been published. Identifying the 100 or more Ptilotus species using morphological characters has been difficult because plants often exhibit slight morphological differences and intermediate characteristics common to several species, subspecies, varieties and forms. Ptilotus exaltatus Nees and P. nobilis ( Lindl) F. Muell share many morphological characteristics, but are classified as different species predominantly based on inflorescence colour. The current study involved a molecular phylogenetic analysis of 14 Ptilotus species using sequence data from the internal transcribed spacer ( ITS) regions ITS 1 and ITS 2 within the 18S-26S nuclear rDNA. Of the 39 accessions analysed, all except those identified as P. exaltatus and P. nobilis clustered according to their respective species based on their morphological taxonomy. In contrast, all 18 P. exaltatus and P. nobilis accessions formed a distinct monophyletic clade with 99% bootstrap values and a low level of sequence variation ( GD=0.002). Taking into account the lack of reliable morphological characters for separating P. exaltatus and P. nobilis, together with the ITS sequence data showing little genetic divergence or genetic structure, we propose that P. exaltatus and P. nobilis are conspecific.
... Noyes and Rieseberg (1999), based on an ITS phylogenetic tree), demonstrated that shrubs or trees, such as in the genus Olearia, were ancestral and that herbaceous genera such as Minuria and Calotis were derived in the Australian Astereae. According to comparison of the ITS and matK sequences, the genus Calotis has accumulated the fewest unique mutational changes among Australian Astereae genera examined, such as Brachycome (Denda et al. 1999), Minuria (Lowrey et al. 2001), Olearia (Cross et al. 2002), Podolepis (Konishi et al. 2000) and Vittadinia (Lowrey et al. 2001). Thus, speciation in the genus Calotis appears to be recent with a rapid divergence from one another. ...
... A similar array of chromosome number reduction found in the Australian genera of Brachycome (Smith-White et al. 1970;Watanabe et al. 1999a), Podolepis (Turner 1970;Konishi et al. 2000), Pogonolepis (Short 1986), Trichanthodium (Short 1990) and many other genera of Gnaphalieae (Watanabe et al. 1999b) in the arid or semiarid regions under the Mediterranean climate. In such areas, seeds may spend from a few to many years in the ground before germinating and the aging seed bank serves as a source of chromosomal variation because of the accumulation of many chromosomal mutations (Levin 2002). ...
The intra-generic relationships of the Australian genus Calotis, with various chromosome base numbers from x = 8 to x = 4, were examined by the comparison of nucleotide sequences of the complete ITS region of nuclear rDNA and of the matK gene of chloroplast DNA. Within a monophyletic Calotis, four lineages were identified. Reconstruction of ancestral states suggests that the chromosome base number for Calotis is x = 8. Dysploidal reductions in chromosome base number from x = 8 to x = 7 and from x = 8 to x = 5 or 4 have occurred independently at least three times. Lower base numbers of x = 7, 5, and 4 are found predominantly in the arid and semi-arid zone species of Central and Western Australia. Total karyotypic length (genome size) is greater in perennials than in annuals within the genus Calotis. The elaborated pappus and surface structures of cypsela, and life form of species seem to be homoplasous with multiple origins in the evolutionary history of the lineage.
... (Bayer et al. 1996), Podolepis Labill. (Konishi et al. 2000) and Anaphalis DC. (Glenny and Wagstaff 1997), and recently for inferring the phylogeny of Australian and New Zealand genera of the Gnaphalieae (Breitwieser et al. 1999). Other regions of the nuclear rDNA, the ETS, and of the chloroplastic DNA, the trnL intron, the trnL/trnF intergenic spacer and the matK, have also been used in other works on the phylogeny of the Gnaphalieae (Bayer et al. 2000(Bayer et al. , 2002. ...
The internal transcribed spacers ITS1 and ITS2 of the nuclear rDNA were sequenced for 41 Helichrysum species (Gnaphalieae), focusing on the Mediterranean group of species, together with eight representatives of other genera of the Gnaphalieae, in order to check the hypothesised monophyly of the Mediterranean Helichrysum group and the correspondence of the sequence data with its traditional sectional classification. The cladistic analysis of sequence data supports monophyly of the Mediterranean Helichrysum excluding H. frigidum and H. montelinasanum. The traditional classification of the Mediterranean species into two sections, Helichrysum and Virginea, is not supported, whereas a group constituted by species from the west Mediterranean area is shown as a moderately supported monophyletic clade in the strict consensus tree. Other results also show and confirm the complexity, still not satisfactorily resolved, of the Helichrysum generic delimitation: Pseudognaphalium luteoalbum appears merged in Helichrysum whereas Helichrysum dasyanthum appears more related to Anaxeton laeve than to any Helichrysum species.
