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302 results for “plastid”
Data from: Evolution of the plastid genomes in diatoms
Diatoms are a monophyletic group of eukaryotic, single-celled heterokont algae. Despite years of phylogenetic research, relationships among major groups of diatoms remain uncertain. Here we assess diatom phylogenetic relationships using the plastid genome (plastome). The 22 previously published diatom plastomes showed variable genome size, gene content and extensive rearrangement. We report another 18 diatom plastome sequences ranging in size from 119,120 to 201,816 bp. Plagiogramma staurophorum had the largest plastome sequenced so far due to large inverted repeats and a 2971 bp group II intron insertion in petD. The previously reported loss of psaE, psaI and psaM genes in Rhizosolenia imbricata also occurred in the closely related species Rhizosolenia fallax. In the largest genome-scale phylogeny yet published for diatoms based on 103 shared plastid-coding genes from 40 diatoms and Triparma laevis as the outgroup, Leptocylindrus was recovered as sister to the remaining diatoms and the clade of Attheya plus Biddulphia was recovered as sister to pennate diatoms, strongly rejecting monophyly of two of the three proposed classes of diatoms. Our study also revealed extensive gene loss and a strong positive correlation between sequence divergence and gene order change in diatom plastomes.
the supplementary of Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates
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Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
<p><strong>Aim</strong>: Miombo woodlands form a characteristic vegetation type covering 2.7 million km<sup>2</sup> in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of <em>Brachystegia</em> trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo-Congolian rain forests (8 species).</p> <p><strong>Location</strong>: Tropical Africa, Guineo-Congolian forests and Zambezian savannahs.</p> <p><strong>Methods</strong>: We used a genome skimming approach to sequence the plastomes of 45 <em>Brachystegia</em> samples, covering 25 of the 29 existing species, and one outgroup (<em>Julbernardia paniculata</em>). The phylogeny of the plastomes was reconstructed and time-calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographic distances using Mantel tests. Finally, we inferred the evolutionary history of <em>Brachystegia</em> based on the age and spatial distribution of its lineages.</p> <p><strong>Results</strong>: Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East-West axis, ranging from Angola to East Africa. Their divergence started from the Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma).</p> <p><strong>Main Conclusions</strong>: <em>Brachystegia</em> plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo <em>Brachystegia</em>, and possibly of miombo vegetation, during the Plio-Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridisation events between species. </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>
A New Model and Dating for the Evolution of Complex Plastids of Red Alga Origin
<p>The zip files includes alignments of protein sequences in fasta format (SequenceAlignments.zip) and their concatenated sets used in our research project (ConcatenatedAlignments.zip). Additionally, we included raw (unaligned) protein sequences in fasta format (RawSequences.zip). In total, we employed 97 amino acid sequences of conserved plastid-encoded proteins, carefully selected from the NCBI reference sequence database (<a href="https://www.ncbi.nlm.nih.gov/refseq/">https://www.ncbi.nlm.nih.gov/refseq/</a>), and GenBank (<a href="https://www.ncbi.nlm.nih.gov/genbank/">https://www.ncbi.nlm.nih.gov/genbank/</a>), representing 112 organisms. Our dataset included 111 eukaryotes carrying red-alga derived plastids and the closest plastid cyanobacterial relative <i>Gloeomargarita lithophora</i> Alchichica D10. We performed independent alignments of each homologous protein group using a slow and accurate L-INS-i algorithm implemented in MAFFT v7.429 (<a href="https://doi.org/10.1093/molbev/mst010">https://doi.org/10.1093/molbev/mst010</a>). The resulting multiple sequence alignments were carefully assessed using AliView (<a href="http://dx.doi.org/10.1093/bioinformatics/btu531">http://dx.doi.org/10.1093/bioinformatics/btu531</a>), and phylogenetically informative sites were selected through trimAl <a href="https://doi.org/10.1093/bioinformatics/btp348">https://doi.org/10.1093/bioinformatics/btp348</a>and ClipKIT (<a href="https://doi.org/10.1371/journal.pbio.3001007">https://doi.org/10.1371/journal.pbio.3001007</a>). The trimmed alignments were concatenated into supermatrices using SequenceMatrix 1.8 (<a href="https://doi.org/10.1111/j.1096-0031.2010.00329.x">https://doi.org/10.1111/j.1096-0031.2010.00329.x</a>)to generate comprehensive datasets for phylogenetic and molecular clock analyses. We also generated a supermatrix composed of untrimmed alignments.</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>
Data from: Remarkably conserved plastid genomes of Quercus Group Cerris in China: comparative and phylogenetic analyses
Quercus is one of the most important genera for considering its economic and ecological values, with approximately 500 species worldwide. Quercus group Cerris is endemic to Eurasia (including 11 species), and three species (Quercus acutissima, Quercus chenii and Quercus variabilis) are widely distributed in China. Here, we sequenced the complete plastid genomes of Q. acutissima and Q. chenii by Illumina pair-end sequencing, and obtained an additional plastome of Q. variabilis from GenBank. Although geographically distant sampling, the three plastomes in group Cerris were remarkably conserved with regard to genome size, gene organization, GC content, and IR/SC boundary regions. The phylogenetic analysis showed that group Cerris nested in group Ilex, forming a Cerris-Ilex clade. The current study provided plastid genomic-scale data for the less intensively studied group Cerris, which would be useful for studying speciation processes, geographical structure and phylogeny within the group Cerris in the future.
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>
Dating the origin and spread of plastids and chromatophores
<p class="MsoNormal"><span>Photosynthetic eukaryotes have shaped the Earth's biosphere by producing </span><span>oxygen</span><span> </span><span>and converting light into organic compounds in specialized organelles called plastids. Plastids evolved from free-living cyanobacteria ingested by heterotrophic unicellular eukaryotes. Two such independent engulfment processes, called cyanobacterial endosymbioses, have been reported so far. The first gave rise to primary plastids and three Archaeplastida lineages: glaucophytes, red algae and green algae with land plants, whereas the second resulted in chromatophores in the rhizarian amoeba <em>Paulinella</em>. Importantly, archaeplastidans donated their plastids to many protist groups, thereby further spreading photosynthesis across the tree of life. To reveal the complex plastid evolution, we performed comprehensive phylogenetic and multi-clock analyses based on new </span><span>fossil </span><span>calibration points and </span><span>the greatest number yet of </span><span>plastid-encoded proteins from 108 taxa, representing a large diversity of photosynthetic organisms. Our results indicate that primary plastids evolved prior to 2.1 - 1.8 Ba, i.e. before glaucophytes diverged from the other archaeplastidans, and <em>Paulinella</em> chromatophores most probably before 292 - 266 Ma. Red and green algae were engulfed by cryptophyte and </span><span>chlorarachniophyte </span><span>ancestors between 1.7 - 1.4 Ba, and </span><span>1.1 - 1.0 Ba, respectively;</span><span> the former subsequently triggered </span><span>plastid transfers to other eukaryotes. </span><span>We also studied the impact of various molecular clocks and calibration sets on the age estimation and clearly indicate that the clocks are the source of greater differences.</span></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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Dating the origin and spread of plastids and chromatophores
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<em>Terniopsis chanthaburiensis</em> (Podostemaceae), a new record for China and its complete plastid genome
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Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae
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Prey morphotype and abundance controls plastid retention and bloom dynamics for a mixotrophic dinoflagellate
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Data from: NOVOWrap: an automated solution for plastid genome assembly and structure standardization
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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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