Journal of Plant Research, Journal Year: 2023, Volume and Issue: 136(3), P. 291 - 304
Published: Feb. 20, 2023
Language: Английский
BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)
Published: Jan. 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
Language: Английский
Citations
44
The Plant Journal, Journal Year: 2022, Volume and Issue: 111(1), P. 117 - 133
Published: April 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.
Language: Английский
Citations
50
Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13
Published: March 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.
Language: Английский
Citations
44
BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)
Published: Jan. 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.
Language: Английский
Citations
36
International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(2), P. 536 - 536
Published: Jan. 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.
Language: Английский
Citations
1
International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3606 - 3606
Published: Feb. 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
Language: Английский
Citations
18
BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)
Published: July 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.
Language: Английский
Citations
24
International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(19), P. 11617 - 11617
Published: Oct. 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.
Language: Английский
Citations
23
Journal of Molecular Evolution, Journal Year: 2023, Volume and Issue: 91(2), P. 156 - 168
Published: March 1, 2023
Language: Английский
Citations
16
Phytomedicine, Journal Year: 2024, Volume and Issue: 131, P. 155770 - 155770
Published: May 29, 2024
Language: Английский
Citations
5