The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

BMC Genomics, Год журнала: 2022, Номер 23(1)

Опубликована: Июнь 29, 2022

Okra (Abelmoschus esculentus L. Moench) is an economically important crop and known for its slimy juice, which has significant scientific research value. The A. chloroplast genome been reported; however, the sequence of mitochondrial still lacking.

Язык: Английский

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Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

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

Опубликована: Фев. 23, 2022

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one most extraordinarily diverse clades among angiosperms. Papilionoids are a major source food forage, ecologically successful in all biomes, display dramatic variation both floral architecture plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding relationships groups Papilionoideae, yet backbone phylogeny remains unresolved. In this study, we sequenced assembled 39 new plastomes that covering key representing morphological diversity subfamily. From 244 total taxa, produced eight datasets for maximum likelihood (ML) based on entire and/or concatenated sequences 77 protein-coding (CDS) two multispecies coalescent (MSC) individual gene trees. We additionally combined nucleotide dataset comprising CDS plus matK only, which papilionoid were sampled. A ML tree plastome maximally supported deep recent divergences papilionoids (223 out 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, Amburaneae), Cladrastis, Andira, Exostyleae formed grade to remainder concordant with nine MSC Phylogenetic remaining five lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because insufficient support conflicting Our study fully resolved nodes however, some require further exploration. More genome-scale data rigorous needed disentangle lineages.

Язык: Английский

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Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 199, С. 108138 - 108138

Опубликована: Июль 6, 2024

Язык: Английский

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Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(12), С. 6786 - 6786

Опубликована: Июнь 20, 2024

Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. ecologically valuable for their roles windbreaking sand fixation. However, the taxonomy phylogenetic relationships of genus still unclear. In this study, we sequenced assembled chloroplast genomes representative reconstructed robust at section level. The genome has lost inverted repeat region wascategorized loss clade (IRLC). eight ranged from 128,458 bp to 135,401 contained 110 unique genes. All have a highly conserved structure gene order. number long repeats simple sequence (SSRs) showed significant variation among species, indicating heterogeneous evolution Caragana. Selective pressure analysis genes revealed most protein-coding evolved under purifying selection. analyses indicated each forms clade, except Spinosae, which was divided into two clades. This study elucidated within widely detailed information obtained can serve as resource understanding molecular dynamics

Язык: Английский

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Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses

Journal of Systematics and Evolution, Год журнала: 2022, Номер 61(1), С. 22 - 41

Опубликована: Июль 25, 2022

Abstract The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised the genera Glycyrrhiza and Glycyrrhizopsis . Some taxa contain glycyrrhizin, pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling to reconstruct phylogenetic relationships based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, low‐copy DNA. We launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. integrated results indicated should be split from , while former genus Meristotropis treated as part includes two species, asymmetrica flavescens recognize 13 : acanthocarpa astragalina bucharica echinata foetida glabra gontscharovii lepidota macedonica pallidiflora squamulosa triphylla yunnanensis propose broader G. aspera s.s., inflata uralensis represents glycyrrhizin‐contained medicinal group. Our ancestral state inferences show ancestor lacked presence glycyrrhizin evolved twice within during last million years. integrative phylogenomics‐MLA study not only provides new insights into long‐standing controversies Glycyrrhizeae, but useful approach future studies other plant taxa.

Язык: Английский

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Molecular phylogeny and spatio‐temporal diversification of the Millettioid/Phaseoloid clade (Fabaceae: Papilionoideae)

Journal of Systematics and Evolution, Год журнала: 2024, Номер 62(6), С. 1103 - 1117

Опубликована: Апрель 24, 2024

Abstract The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of subfamily Papilionoideae (Fabaceae) that poorly understood in terms its diversification and biogeographic history. To fill this gap, we generated time‐calibrated phylogeny for 749 species representing c . 80% genera using nrDNA ITS, plastid matK , plastome sequence (including 38 newly sequenced plastomes). Using phylogenetic framework, explored clade's temporal reconstructed ancestral areas dispersal events. Our analyses support monophyly four tribal lineages (Abreae, Desmodieae, Indigofereae, Psoraleeae), while two sensu lato millettioids phaseoloids are polyphyletic. fossil‐calibrated dating analysis showed nearly simultaneous divergence between stem node ( 62 Ma) crown 61 Paleocene. suggested originated Africa dispersed to Asia, Europe, Australia, Americas at different periods Cenozoic. We found evidence shifts rates across throughout Cenozoic, with rapid increase net since 10 Ma. Possible explanations present‐day richness distribution include boreotropical migration, frequent intra‐ intercontinental long‐distance dispersals elevated speciation following Mid‐Miocene Climatic Optimum. Together, these results provide novel insights into patterns clade, setting stage future evolutionary research on important legume clade.

Язык: Английский

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Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Фев. 6, 2025

The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), emergence Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited data incomplete research, highlighting need for systematic investigation. This study presents an in-depth analysis cpDNAs Pap., with aim unraveling interconnections among its species. Complete 18 species were sequenced using Illumina Novaseq 6000 platform, followed by assembly annotation. Comparative analyses conducted elucidate structural variations relationships. research uncovered differences characteristics Pap.. lengths range from 121,190 bp 158,539 bp, they contain between 107 112 unique genes. Five species, namely Desmodium elegans Indigofera bracteata, exhibit typical quadripartite structure, while thirteen genera such as Astragalus (Ast.), Hedysarum (Hed.), Caragana (Car.) are grouped (IRLC). Genetic characteristic revealed plentiful presence SSR loci, single-nucleotide repeats dinucleotide (A/T) being most predominant. Notably, five including D. have experienced rearrangements. For example, inversion approximately 23 kilobase (kb) pairs was observed Pueraria peduncularis Sophora moorcroftiana. These pronounced their non-coding regions. at cpDNA sites identified. Moreover, reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), Ka/Ks ratio all protein-coding determined be less than 1. topological constructed tree 85 basically consistent that Seven main clades formed relatively bootstrap values exhibited, further clarifying them. provides novel insights into phylogeny offering foundational resource future taxonomic research.

Язык: Английский

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Phylogenomic and morphological evidence supports the reinstatement of the bamboo genus Clavinodum from Oligostachyum (Poaceae: Bambusoideae)

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер unknown, С. 108327 - 108327

Опубликована: Март 1, 2025

Язык: Английский

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Essential roles of nodule cysteine‐rich peptides in maintaining the viability of terminally differentiated bacteroids in legume–rhizobia symbiosis

Journal of Integrative Plant Biology, Год журнала: 2025, Номер unknown

Опубликована: Март 19, 2025

ABSTRACT Investigations into the nitrogen‐fixing symbiosis between legumes and rhizobia can yield innovative strategies for sustainable agriculture. Legume species of Inverted Repeat‐Lacking Clade (IRLC) Dalbergioids, utilize nodule cysteine‐rich (NCR) peptides, a diverse family peptides characterized by four or six highly conserved cysteine residues, to communicate with their microbial symbionts. These many which exhibit antimicrobial properties, induce profound differentiation bacteroids (semi‐autonomous forms bacteria) within cells. This terminal endows ability fix nitrogen, at expense reproductive capacity. Notably, significant number NCR is expressed in fixation zone, where have already reached differentiation. Recent discoveries, through forward genetics approaches, revealed that functions extend beyond effects promotion They also play critical role sustaining viability terminally differentiated findings underscore multifaceted highlight importance these mediating communications host cells bacteroids.

Язык: Английский

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Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae

Genetica, Год журнала: 2025, Номер 153(1)

Опубликована: Май 6, 2025

Язык: Английский

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