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47 results for “plastid phylogenomics”
Data from: Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics
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Phylogenomic insights into the origin of primary plastids
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Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
<p>Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support, and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevents the confident resolution of these nodes using plastome data alone.</p>
Highly resolved papilionoid legume phylogeny based on plastid phylogenomics
<p>Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera of evolution and morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. An ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.</p>
Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
<p>In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that, while ILS could by itself explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are with few exceptions highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.</p>
Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae
<p>Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (~23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (<em>Apinagia</em>, <em>Marathrum</em>, <em>Oserya</em>, and <em>Podostemum</em>), as well as four species, are not monophyletic. In particular, we show that <em>Podostemum flagelliforme</em> should not be included in <em>Podostemum and is better recognized as Devillea flagelliformis, </em>and that <em>Marathrum capillaceum</em> is embedded within <em>Lophogyne </em>s.l.<em> </em>and should be recognized as <em>Lophogyne capillacea</em>. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical genera <em>Diamantina</em>, <em>Ceratolacis</em>, <em>Cipoia,</em> and <em>Podostemum</em> are resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome.</p>
Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)
Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, <i>Cephalostachyum </i>and <i>Schizostachyum</i>, were paraphyletic. Species of <i>Cephalostachyum</i> were resolved in two successive basal clades, while <i>Annamocalamus</i> was embedded in the <i>Schizostachyum</i> clade. Different plastid regions provided inconsistent signals for the relationship of <i>Melocanna</i> and <i>Pseudostachyum</i>. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long-branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: <i>in situ</i> diversification on the Asian mainland; dispersing southwest to Sri Lanka and to the Western Ghats in South India; and spreading southeast to Malesia and Oceania via the Indo-China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea-level-fall events since the late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of <i>Schizostachyum</i>.
Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions
<p><em>Medicago</em> <em>truncatula</em> is a model legume that has been extensively investigated in diverse subdisciplines of plant science. <em>Medicago</em> <em>littoralis</em> can interbreed with <em>M</em>. <em>truncatula</em> and <em>M</em>. <em>italica</em>; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that <em>M</em>. <em>truncatula</em> accessions are heterogeneous, but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse <em>M</em>. <em>truncatula</em> accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both <em>M</em>. <em>truncatula</em> and <em>M</em>. <em>littoralis</em>. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a <em>M</em>. <em>italica</em> subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the <em>M</em>. <em>littoralis</em> subclade. Our results suggest that the <em>M</em>. <em>truncatula</em> accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.</p>
New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
<p>The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out-of-Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of <em>Lonicera</em> shows a typical Europe-Asia-North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section <em>Isika</em> polyphyletic, while sections <em>Nintooa</em>, <em>Isoxylosteum</em>, and <em>Coelxylosteum</em> were monophyletic in subgenus <em>Chamaecerasus</em>. Based on the nuclear and chloroplast phylogeny, we suggest transferring L. <em>maximowiczii</em> and L. <em>tangutica</em> into section <em>Nintooa</em>. Reconstruction of ancestral areas suggests that <em>Lonicera</em> originated in the Qinghai-Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of <em>Lonicera</em> in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of <em>Lonicera</em>.</p>
Polytomous radiation revealed in phylogenomic analysis of Allium (Amaryllidaceae) plastid genomes
<p>Alignment of 115 <em>Allium </em>chloroplast genomes plus three outgroups with all sites with missing data masked.</p>
Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
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Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae
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Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics
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Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)
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Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
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Highly resolved papilionoid legume phylogeny based on plastid phylogenomics
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Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions
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Data from: Plastid phylogenomics of the tribe potentilleae (Rosaceae)
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New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
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Data from: First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)
Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75 million years. However, despite significant taxon sampling, combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs. Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show that the use of a de novo assembled plastome from within the genus provides less ambiguity and higher coverage across the 59 Ficus and 6 outgroup plastome assemblies compared to using the nearest available reference plastome outside the genus resulting in improved resolution and higher support of the phylogenetic relationships within Ficus inferred from plastome data. Chloroplast genome data confidently resolved relationships among major groups of figs and largely support current understanding based on nuclear sequence data including passively pollinated Neotropical section Pharmacosycea as sister lineage to all other Ficus. However, conflicts between the new plastome topology and previous nuclear studies are observed for both individual species as well as relationships among some sections at deeper levels. Conflicts could be caused by lack of resolution in the nuclear data or may indicate potential cyto-nuclear discordance as previously observed in an African lineage of Ficus.
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