Plastome Diversity and Phylogenomic Relationships in Asteraceae.
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ABSTRACT:
SUBMITTER: Pascual-Diaz JP
PROVIDER: S-EPMC8705268 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), along with a total of 51-61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of Dolomiaea as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, rpoC2 and ycf1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.
| S-EPMC7174903 | biostudies-literature
Project description:Reichardia Roth is a small Mediterranean genus comprising ten homogeneous species with basic chromosome numbers of 7, 8, and 9. To assess the plastid genome evolution and differentiation of Reichardia species, we assembled the complete plastome sequences of seven Reichardia and two Launaea species and conducted various phylogenomic analyses comparatively with nuclear ribosomal DNA ITS sequences. Reichardia and Launaea plastomes were highly conserved in gene content and order, containing 130 genes. Plastid phylogenomic reconstruction strongly suggested that Reichardia was a sister to Launaea, and its common ancestor initially diverged into two major lineages: the first containing species with n = 8 chromosomes exclusively, and the other with n = 9, 8, and 7 chromosomes. Although the ancestral Reichardia karyotype was suggested to most likely be n = 9 from ancestral chromosome number reconstruction, the pattern of descending dysploidy indicated by the phylogenetic trees based on nuclear ribosomal DNA ITS was less evident in the trees based on the plastome. Possible reasons for these findings are discussed.
| S-EPMC9247168 | biostudies-literature
Project description:BackgroundSaussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera.ResultsAll Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability.ConclusionsOur analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.
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Project description:Myripnois is a monotypic shrub genus in the daisy family constricted to northern China. Although wild populations of Myripnois dioica are relatively rare, this plant may potentially be cultured as a fine ornamental. In the present study, we sequenced the complete plastome of M. dioica, generating the first plastome sequences of the subfamily Pertyoideae. The plastome of M. dioica has a typical quadripartite circular structure. A large ?20-kb and a small ?3-kb inversion were detected in the large single copy (LSC) region and shared by other Asteraceae species. Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups, corresponding to four Asteraceae subfamilies: Asteroideae, Cichorioideae, Pertyoideae and Carduoideae. Among these four subfamilies, Pertyoideae is sister to Asteroideae + Cichorioideae; Carduoideae is the most basal clade. In addition, we characterized 13 simple sequence repeats (SSRs) that may be useful in future studies on population genetics.
| S-EPMC6951274 | biostudies-literature
Project description:Arecaceae is a species-rich clade of Arecales, while also being regarded as a morphologically diverse angiosperm family with numerous species having significant economic, medicinal, and ornamental value. Although in-depth studies focused on the chloroplast structure of Arecaceae, as well as inferring phylogenetic relationships using gene fragments, have been reported in recent years, a comprehensive analysis of the chloroplast structure of Arecaceae is still needed. Here we perform a comprehensive analysis of the structural features of the chloroplast genome of Arecaceae, compare the variability of gene sequences, infer phylogenetic relationships, estimate species divergence times, and reconstruct ancestral morphological traits. In this study, 74 chloroplast genomes of Arecaceae were obtained, covering five subfamilies. The results show that all chloroplast genomes possess a typical tetrad structure ranging in size between 153,806-160,122 bp, with a total of 130-137 genes, including 76-82 protein-coding genes, 29-32 tRNA genes, and 4 rRNA genes. Additionally, the total GC content was between 36.9-37.7%. Analysis of the SC/IR boundary indicated that the IR region underwent expansion or contraction. Phylogenetic relationships indicate that all five subfamilies in Arecaceae are monophyletic and that Ceroxyloideae and Arecoideae are sister groups (BS/PP = 100/1). The results of molecular dating indicate that the age of the crown group of Arecaceae is likely to be 96.60 [84.90-107.60] Ma, while the age of the stem group is 102.40 [93.44-111.17] Ma. Reconstruction of ancestral traits indicate that the ancestral characteristics of the family include monoecious plants, one seed, six stamens, and a smooth pericarp.
| S-EPMC9552784 | biostudies-literature
Project description:Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.
| S-EPMC7335403 | biostudies-literature
Project description:BackgroundPolypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference.ResultsThe phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene.ConclusionThis study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives.
| S-EPMC9628275 | biostudies-literature
Project description:In this study, we created several datasets using new publicly released as well as newly-generated DNA and RNA-seq data for representatives of all cnidarian classes to test all previously-proposed phylogenetic hypotheses. We explored two popular orthology assessment methods to build gene alignments for phylogenetic purposes, and compared their outcomes regarding both gene representation and phylogenetic signal (aka species trees). Our Cnidaria dataset is the most extensive to date, including sequence-rich datasets for three Staurozoa species and one Ceriantharia.
| PRJEB19215 | ENA
Project description:BackgroundSeahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved.ResultsHere, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea.ConclusionsOur results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events.
| S-EPMC8962102 | biostudies-literature
Project description:BackgroundBambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.ResultsHere a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.ConclusionsPhylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.
| S-EPMC4389303 | biostudies-literature