BMC Plant Biology, Год журнала: 2025, Номер 25(1)
Опубликована: Май 1, 2025
Язык: Английский
BMC Genomics, Год журнала: 2023, Номер 24(1)
Опубликована: Янв. 18, 2023
The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and Far East Asia. This contains about 100-150 species, with many species valued as important agricultural, medicinal horticultural resources. However, genomic resources suitable molecular markers for identification are currently sparse.We conducted comparative genomics phylogenetic analyses on species. chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist a large single copy (LSC, 86,986-88,200 bp), small (SSC, 15,498-15,891 pair inverted repeats (IRs, 29,765-29,934 bp). genomes contain 113 unique genes, including 79 protein coding 30 tRNA 4 rRNA genes. structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long conservative Zingiber. analysis divergence indicates following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 ycf3). Eight highly variable regions identified seven intergenic (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA ndhF-rpl32) one genic (ycf1). revealed sect. was sister to Cryptanthium rather than Pleuranthesis.This study reports 14 complete Overall, this provided solid backbone phylogeny polymorphisms we have uncovered sequencing offer rare possibility (for Zingiber) generation DNA markers. These results provide foundation future studies seek understand evolutionary dynamics or individual population variation
Язык: Английский
Процитировано
45
The Plant Journal, Год журнала: 2022, Номер 111(1), С. 117 - 133
Опубликована: Апрель 19, 2022
SUMMARY Serine carboxypeptidase‐like acyltransferases (SCPL‐ATs) play a vital role in the diversification of plant metabolites. Galloylated flavan‐3‐ols highly accumulate tea ( Camellia sinensis ), grape Vitis vinifera and persimmon Diospyros kaki ). To date, biosynthetic mechanism these compounds remains unknown. Herein, we report that two SCPL‐AT paralogs are involved galloylation flavan‐3‐ols: CsSCPL4, which contains conserved catalytic triad S‐D‐H, CsSCPL5, has alternative T‐D‐Y. Integrated data from transgenic plants, recombinant enzymes, gene mutations showed CsSCPL4 is acyltransferase, while CsSCPL5 non‐catalytic companion paralog (NCCP). Co‐expression likely responsible for galloylation. Furthermore, pull‐down co‐immunoprecipitation assays interact, increasing protein stability promoting post‐translational processing. Moreover, phylogenetic analyses revealed their homologs co‐exist galloylated flavan‐3‐ol‐ or hydrolyzable tannin‐rich species. Enzymatic further necessity co‐expression those acyltransferase activity. Evolution analysis residues may have taken place about 10 million years ago. These findings show SCPL‐ATs NCCPs contributes to acylation kingdom.
Язык: Английский
Процитировано
52
Frontiers in Genetics, Год журнала: 2022, Номер 13
Опубликована: Март 10, 2022
Theaceae species are dicotyledonous angiosperms with extremely high ornamental and economic value. The chloroplast genome is traditionally used to study evolution, expression of genes transformation. Codon usage bias (CUB) analysis beneficial for investigations evolutionary relationships can be improve gene efficiency in genetic transformation research. However, there relatively few systematic studies the CUB genomes species. In this study, nucleotide compositions parameters were determined by scripts written Perl language, CodonW 1.4.2, CU.Win2000, RStudio SPSS 23.0. data 40 obtained analyse codon (CU) characteristics coding regions influence source variation on CUB. To explore relationship between levels these plastomes, synonymous order (SCUO) measure independent length composition (MILC) values determined. Finally, phylogenetic revealed among Our results showed that based species, was codons containing A/T bases those ended bases. Moreover, great commonality according comparative relative (RSCU) frequency (RFSC): had 29 identical (RSCU > 1), 19 high-frequency codons. mainly affected natural selection. SCUO value 0.23 or 0.24, level moderate, MILC values. Additionally, we observed a positive correlation values, which indicated might affect expression. Furthermore, conserved. A provides further evidence their evolution phylogeny.
Язык: Английский
Процитировано
45
BMC Plant Biology, Год журнала: 2023, Номер 23(1)
Опубликована: Янв. 14, 2023
Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to high intraspecific diversity low interspecific variation in morphological characters species within this genus. In study, 22 samples representing 15 from China, were sequenced combined published test phylogenetic resolution using complete chloroplast genome. Furthermore, comparative analyses genomes performed investigate genome evolution Eriocaulon.The nine proved highly similar size, gene content, order. The exhibited typical quadripartite structures lengths 150,222 bp 151,584 bp. Comparative revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, ycf1) could serve as effective molecular markers for further identification species. Phylogenetic results supported monophyletic group. identified relationships taxonomic treatment section Heterochiton Leucantherae, was first divergent tree divided into five clades. divergence times indicated all sections diverged later Miocene most extant Quaternary. phylogeny rapid radiation occurred history Eriocaulon.Our study mostly at level China demonstrated power whole sequences. developed can help us better identify understand evolutionary future.
Язык: Английский
Процитировано
40
International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(2), С. 536 - 536
Опубликована: Янв. 10, 2025
Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only great ornamental value and one world's top three flower bedding but also have wide range medicinal edible uses. Currently, taxonomy phylogenetic relationships species still controversial. In order to better understand their chloroplast properties evolution, nine (Impatiens repens, rectirostrata, baishaensis, rostellata, faberi, oxyanthera, tienchuanensis, blepharosepala, distracta) were sequenced, complete genomes analysed. Nine ranged length from 150,810 bp (I. rectirostrata) 152,345 blepharosepala). The all typical circular DNA molecules, GC content each region was consistent with published plants. results showed that seven mutational hotspots (trnL-UAG, ndhG, ycf1, ccsA, rrn23, trnA-UGC, ycf2) could be used as supporting data for further analyses tree identification. addition, support Balsaminaceae monophyletic taxon, Hydrocera triflora at base branch, original sister group relationship species. this paper enrich genomes, availability these will provide rich genetic information identification, thus enhancing taxonomic accuracy resolution Impatiens, promoting investigation rational use plant resources.
Язык: Английский
Процитировано
2
Journal of Molecular Evolution, Год журнала: 2023, Номер 91(2), С. 156 - 168
Опубликована: Март 1, 2023
Язык: Английский
Процитировано
19
International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(4), С. 3606 - 3606
Опубликована: Фев. 10, 2023
Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors cultivars. It has been cultivated for nearly 1600 years essential investigating the germplasm assessing genetic variation to support international cultivar identification breeding programs. In this study, 20 common cultivars from different varietal groups morphologies, as well multiple wild relative species, were analyzed investigate maternal donor of discover relationships among based on plastome nuclear ribosomal DNA (nrDNA) sequences. A total 47 single nucleotide polymorphisms (SNPs) 24 insertion/deletions (indels) identified in cultivars' 25 SNPs nrDNA. Phylogenetic analysis sequences showed that all formed clade species indica, indicating was Population structure PCA analyses supported two clades cultivars, which exhibited significant differences according dataset. The results nrDNA divided into three most had at least backgrounds higher gene flow. Our suggest can be used molecular markers
Язык: Английский
Процитировано
18
BMC Plant Biology, Год журнала: 2025, Номер 25(1)
Опубликована: Март 12, 2025
Camellia reticulata Lindl. (C. reticulata) is the tallest ornamental camellia globally, with wild populations comprising a polyploid complex of diploids (2×), tetraploids (4×), and hexaploids (6×). The type specimen C. heteroploid hexaploid derived from 2 × ancestors, including pitardii, saluenensis, reticulata. Currently, limited information exists regarding evolutionary characteristics chloroplast genomes at different ploidy levels, phylogenetic position 4 remains unclear. This study sequenced, assembled, annotated reticulata, comparing them those 6 other closely related species. results indicated that genome sizes ranged 156,519 to 156,927 bp, gene counts, distributions, GC content, codon usage being similar across levels. ycf1 exhibited significant differentiation among species, was identified as candidate for adaptive evolution in Additionally, 11 highly differentiated intergenic regions were identified, six hotspots variation can serve molecular markers genetic studies populations. Analysis selection pressure four genes under positive selection. Phylogenetic analysis revealed along mairei, formed well-supported clade. distances between its three ancestors relatively small. mairei may have participated allopolyploidization both potential independent classification. These findings provide valuable insights into alterations following allopolyploidization, establishing crucial foundation understanding systematic history various levels
Язык: Английский
Процитировано
1
International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(19), С. 11617 - 11617
Опубликована: Окт. 1, 2022
Uncaria, a perennial vine from the Rubiaceae family, is typical Chinese traditional medicine. Currently, uncertainty exists over Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four species mentioned in Pharmacopoeia scandens (an easily confused counterfeit) were sequenced annotated. findings demonstrated that whole genome genus 153,780–155,138 bp full length, encoding total 128–131 genes, containing 83–86 protein-coding eight rRNAs 37 tRNAs. These regions, which include eleven highly variable loci 31–49 SSRs, can be used to create significant molecular markers for genus. phylogenetic tree was constructed according genes sequences five using methods. topology two trees showed no difference. U. rhynchophylla are clustered one group, while hirsuta macrophylla another group. sessilifructus together with above small clades. New insights on relationship revealed via research species. This study will provide theoretical basis identifying its counterfeits, as well provides initial report contributes elucidating evolution China.
Язык: Английский
Процитировано
25
BMC Genomics, Год журнала: 2022, Номер 23(1)
Опубликована: Июль 27, 2022
Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which a Traditional Chinese Medicine (TCM) that utilized as an antifebrile and detoxicant agent for treatment acute pyogenic infections. Historically, many species with violet flowers have been misused in Ding". recognized taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. adulterants were sampled. A total 24 complete chloroplast (cp) genomes analyzed, among these 5 cp genome sequences downloaded from GenBank 19 genomes, including 2 Ding" purchased local TCM pharmacy, newly sequenced.
Язык: Английский
Процитировано
24