Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

Journal of Systematics and Evolution, Год журнала: 2021, Номер 60(6), С. 1263 - 1280

Опубликована: Июнь 17, 2021

Abstract The olive genus Olea includes c . 30–40 taxa in three subgenera ( , Tetrapilus and Paniculatae ) within the family Oleaceae. Historically, was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus poor resolution clades. These analyses also showed not monophyletic. Reliable identification species is important for both their conservation utilization this economically genus. In study, we used phylogenomic data from genome skimming to resolve relationships identify molecular markers identification. We assembled complete plastomes, nrDNA 26 individuals representing 13 using next‐generation sequencing added 18 publicly available accessions developed nuclear SNPs infer phylogenetic Large‐scale 138 samples tribe Oleeae polyphyly with caudatilimba sharing most recent common ancestor main clade (subgenus ). interspecific owing a possible rapid radiation. By comparing plastome data, identified ycf1 b psbE‐petL as best ‐specific chloroplast DNA barcodes. Compared universal barcodes, specific barcodes super‐barcode exhibited higher discriminatory power. Our results demonstrated power phylogenomics improve intricate provided new insights allow accurate species.

Язык: Английский

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Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae

Molecular Phylogenetics and Evolution, Год журнала: 2021, Номер 163, С. 107235 - 107235

Опубликована: Июнь 17, 2021

Язык: Английский

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Origins of cultivars of Chrysanthemum—Evidence from the chloroplast genome and nuclear LFY gene

Journal of Systematics and Evolution, Год журнала: 2020, Номер 58(6), С. 925 - 944

Опубликована: Сен. 28, 2020

Abstract The origins of cultivated chrysanthemums have attracted considerable attention, but they remain poorly known. Here, we reconstructed the phylogeny representative well‐known cultivars and wild species genus Chrysanthemum using chloroplast genomes nuclear LEAFY gene. Our results suggest that geographic ecological factors may determine opportunities for to be involved in origin cultivars. C. indicum, zawadskii, dichrum, nankingense, argyrophyllum , vestitum were likely directly or indirectly as paternal most chrysanthemum examined this study. Yet, maternal is supported a lineage an extinct its subsequent cultivars, all accessions sampled formed strongly clade, distinct from other plastome tree. Thus, originated multiple hybridizations involving several rather than only two few species, with serving parents. This finding consistent having high rates hybridization gene flow, which has been demonstrated within previous studies; nevertheless, it important unravel role ultimate parent also Tianzhu Funiu Mountains Anhui Henan Provinces China represent cryptic species.

Язык: Английский

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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 181, С. 107727 - 107727

Опубликована: Фев. 7, 2023

Язык: Английский

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Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Окт. 13, 2022

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) North America (NA). Species of have high economic values worldwide their high-quality wood rich healthy factors nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported monophyly Carya its two EA NA major subclades, maternal phylogeny still need be comprehensively evaluated. The variation plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes congeneric species, including recently rediscovered critically endangered C. poilanei. overall assessment revealed highly conservative general structures. Our results indicated that remarkable differences several features are consistent with EA-NA showed relatively diverse matrilineal sources among compared Carya. phylogenies were conducted different regions full-length datasets from 30 plastomes, representing 26 species six genera Juglandoideae Myrica rubra (as root). Six out seven topologies strongly previously reported relationships subclades but displayed significant incongruencies within subclades. tree demonstrated optimal topology geographical especially overlapping distribution areas. plastome-based also taxonomic status five controversial as separate Historical recent introgressive hybridization plastid captures might contribute geographic patterns inconsistencies built datasets, while incomplete lineage sorting could account discordance nuclear genome data-based phylogeny. findings highlight an ideal tool exploring potentially other outcrossing perennial woody plants, resolving relationships.

Язык: Английский

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The complete chloroplast genome sequences of nine melon varieties (Cucumis melo L.): lights into comparative analysis and phylogenetic relationships

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Июль 9, 2024

Melon ( Cucumis melo L.) is one of the most extensively grown horticulture crops world. Based on morphological characters, melon was formerly divided into two subspecies, ssp. and C. agrestis . However, present methods are still inadequate to distinguish between them. The phylogenetic analysis based chloroplast genome sequences could provide essential evidence for classification varieties. We sequenced genomes nine different varieties by Illumina Hiseq performed bioinformatic analyses including repeat element analysis, comparison analysis. results showed that has a typical quadripartite structure conserved across analyzed sequences. Its length ranges 155, 558 156, 569 bp, with total GC content varying from 36.7% 37%. found 127–132 genes in genomes, 85–87 protein-coding regions, 34–37 tRNA 6-8 rRNA genes. molecular structure, gene order, content, codon usage, long repeats, simple sequence repeats (SSRs) were mostly among genomes. Phylogenetic clearly ssp This study not only provides valuable knowledge chloroplasts, but also offers theoretical basis technical support genetic breeding melons.

Язык: Английский

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Biogeography of a Global Plant Invader: From the Evolutionary History to Future Distributions

Global Change Biology, Год журнала: 2024, Номер 30(12)

Опубликована: Дек. 1, 2024

Biological invasions pose a global challenge, affecting ecosystems worldwide and human societies. Knowledge of the evolutionary history invasive species is critical to understanding their current invasion success projecting future spread. However, date, few studies have addressed potential spread invaders simultaneously. In this study, we explored both spatiotemporal dynamic patterns distribution Reynoutria japonica, known as one world's worst plant invaders. We analysed 265 R. japonica samples from its geographical ranges across three continents, using seven chloroplast DNA (cpDNA) markers establish phylogenetic relationships among extant populations. combined these with ecological niche modelling infer historical more recent migration predict changes under climate change. Our results indicate that fluctuations sea level likely facilitated expansion southern Japan continental East Asia in Pliocene, followed by contraction Asian Holocene, activities then enabled linage Europe North America, resulting major clades. Future scenarios suggest northward but shrinking habitat China. thus, demonstrates complex influences climate-driven migrations, on an species.

Язык: Английский

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Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Июль 22, 2022

Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but phylogenetic relationships among their contributions to these cultivars poorly resolved. We collected major Lilium assembled plastome sequences. Our reconstruction using 114 plastid genomes, including 70 representing all sections 42 six hybrid divisions two outgroups, uncovered well-supported genetic within . The were separated into distinct groups (groups A B) associated geographical distribution, which further diversified eight different clades that phylogenetically well supported. Additional support was provided by distributions indels single-nucleotide variants, consistent topology. Archelirion, Sinomartagon III, Leucolirion 6a 6b maternal donors for Oriental hybrids, Asiatic Trumpet Longiflorum respectively. OT hybrids originated from Archelirion 6a, LA derived study provides an basis clarifying infrageneric classification origin in

Язык: Английский

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Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae

Genes, Год журнала: 2022, Номер 13(10), С. 1720 - 1720

Опубликована: Сен. 25, 2022

Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, complete chloroplast genome of A. frutescens was obtained based on sequences generated by Illumina HiSeq. The 149,626 base pairs (bp) in length, containing a pair inverted repeats (IR, 24,510 bp) regions separated small single-copy (SSC, 18,352 sequence and large (LSC, 82,254 sequence. contained 132 genes, consisting 85 coding DNA sequences, 37 tRNA 8 rRNA with nineteen genes duplicated IR region. A comparison analysis among ten species from tribe revealed that size varied, but structure, gene content, oligonucleotide were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, detected. Phylogenetic supported separate genus. findings study will be helpful exploration phylogenetic relationships contribute breeding improvement frutescens.

Язык: Английский

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Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Journal of Systematics and Evolution, Год журнала: 2020, Номер 58(5), С. 710 - 724

Опубликована: Июнь 24, 2020

Abstract Species concept and delimitation are fundamental to taxonomic evolutionary studies. Both inadequate informative sites in the molecular data limited taxon sampling have often led poor phylogenetic resolution incorrect species delineation. Recently, whole chloroplast genome sequences from extensive herbarium specimen samples been shown be effective amend problem. Stachyuraceae a small family consisting of only one genus Stachyurus six 16 species. However, has highly controversial because few generally unstable morphological characters used for classification. In this study, we sampled 69 individuals seven (each with at least three individuals) covering entire diversity, geographic range, variation specimens genome‐wide plastid gene sequencing address delineation genus. We obtained high‐quality DNAs using recently developed DNA reconstruction technique. first assembled four sequences. Based on nuclear ribosomal sequence , designed primers multiplex polymerase chain reaction high throughput 44 loci . Data these internal transcribed spacer were analyses. The results showed that Japanese praecox Siebold & Zucc. was sister rest mainland China, which indicated typical Sino‐Japanese distribution pattern. diagnostic characters, distinct distributional monophyly each clade, redefined following an integrative concept, revised taxonomy based previous reports specimens, particular type specimens. Furthermore, our divergence time estimation suggested split its group Crossosomataceae New World ca. 54.29 Mya, but extant started their diversification 6.85 Mya. Diversification China estimated 4.45 This research provided example specimen‐based phylogenomic approach resolving boundaries taxonomically difficult

Язык: Английский

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