Physiology and Molecular Biology of Plants, Journal Year: 2023, Volume and Issue: 29(5), P. 709 - 724
Published: May 1, 2023
Language: Английский
BMC Genomics, Journal Year: 2020, Volume and Issue: 21(1)
Published: Sept. 10, 2020
Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found moist, shaded valleys mountain slopes. This ideal for studying plant adaptation to low light conditions. Although some progress has been made the systematics biogeography Chrysosplenium, its chloroplast genome evolution remains be investigated.
Language: Английский
Citations
74
Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)
Published: March 27, 2025
ABSTRACT The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera 119 species. However, complete chloroplast genome sequences of species have been reported less frequently. In this study, five were newly sequenced, seven others available genomes added compare the evolution in at subfamily level. results indicated that size ranged from 158,116 159,941 bp, encoding 79 81 protein‐coding genes, four ribosomal RNA 30 31 transfer genes. A robust phylogenetic tree was obtained using genomes, supporting all formed a monophyletic group divided into subfamilies. Exbucklandioideae first diverged within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, Hamamelidoideae, which clade. Furthermore, three new potential DNA barcodes provided: trnH‐psbA , psbJ‐petA ycf1 . This study confirms data provide more accurate confident resolution relationships Hamamelidaceae. These genomic not only enhance understanding but also better
Language: Английский
Citations
1
BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)
Published: June 27, 2023
The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. structural characterization complete chloroplast genomes P. storbatiana wilsonii were analyzed compared with those related taxa provide a better understanding their genomic information on phylogeny.It was shown that had typical quadripartite structure conserved genome arrangements moderate divergence. 145,885 bp 145,445 in length, respectively, shared similar GC content 36.8%. Gene annotations two revealed 109 single-copy genes consistently. In addition, 20 duplicated the inverted regions, 16 each possessed one or more introns, five ndh (NA (D)H dehydrogenase) observed both. Comparative analysis total cp other six confirmed stable sequence identity coding non-coding regions higher variation SC than IR regions. Most protein-coding high degree codon preference. Moreover, 45 discovered positive selection. However, different amplifications these eight species. Phylogenetic based CDS from 60 representing main clades Orchidaceae indicated including stobartiana formed monophyletic clade bootstrap nested tribe Vandeae Epidendroideae, consistent previous studies.The results could insight into plastome evolution phylogenetic relationships Phalaenopsis.
Language: Английский
Citations
21
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: March 3, 2023
The subgenus Cerasus , one of the most important groups in genus Prunus sensu lato comprises over 100 species; however, taxonomic classification and phylogenetic relationships remain controversial. Therefore, it is necessary to reconstruct tree for known species. Here, we report chloroplast (cp) genome sequences 11 species provide insight into evolution plastome. cp genomes (157,571–158,830 bp) displayed a typical quadripartite circular structure. plastomes contain 115 unique genes, including 80 protein-coding four ribosomal RNAs, 31 transfer RNAs. Twenty genes were found be duplicated inverted repeats as well at boundary. conserved non-coding showed significant divergence compared with coding regions. We 12 14 intergenic regions higher nucleotide diversity more polymorphic sites, matK rps16 rbcL - trnQ petN psbM trnL trnF . During plastome evolution, codon profile has been strongly biased toward use A/T third base, leucine isoleucine codons appear frequently. identified strong purifying selection on rpoA cemA atpA petB genes; whereas ccsA rps19 rpoC2 ycf2 ndhI signature possible positive during course evolution. In addition, further analyzed these 57 other congenic related species.Through reconstructing phylogeny tree, that true cherry similar flora China forming distinct group, from which P. mahaleb was separated an independent subclade. Microcerasus genetically closer Amygdalus Armeniaca ( stricto ) than members cherry, japonica tomentosa closely triloba pedunculata However, tianshanica formed clade cerasus fruticosa × canescens ‘Gisela 6’, avium group. These results new insights along potential molecular markers candidate DNA barcodes phylogeographic analyses
Language: Английский
Citations
18
BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)
Published: March 18, 2021
Abstract Background Lima bean ( Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source plant proteins for human diet. As we all know, lima beans have economic value great diversity. However, our knowledge chloroplast genome level limited. Results The was obtained by Illumina sequencing technology first time. Cp with length 150,902 bp, including pair inverted repeats (IRA IRB 26543 bp each), large single-copy (LSC 80218 bp) small region (SSC 17598 bp). In total, 124 unique genes 82 protein-coding genes, 34 tRNA 8 rRNA were identified in P. genome. A total 61 long 290 SSRs detected It has typical 50 kb inversion 70 subtribe Phaseolinae. rpl16 , accD petB rsp16 clpP ndhA ndhF ycf1 coding regions found significant variation, intergenic trnk - rbcL atpB ndhJ rps4 psbD rpoB atpI atpA psbJ psbE psbB rsp11 rsp19 ccsA high degree divergence. phylogenetic analysis showed that appears be more closely related vulgaris V.unguiculata V. radiata . Conclusions characteristics time, these results will provide useful insights species identification, evolutionary studies molecular biology research.
Language: Английский
Citations
35
Genes, Journal Year: 2022, Volume and Issue: 13(9), P. 1550 - 1550
Published: Aug. 28, 2022
Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species genus are widely used for wide range medicinal and industrial aspects. At present, most studies related to gene resources restricted morphological analyses features individual genomes, currently available select molecular markers insufficient. In this study, we assembled annotated complete chloroplast genomes nine species Litsea, carried out series comparative analyses, reconstructed phylogenetic relationships within genus. The genome length ranged from 152,051 152,747 bp total 128 genes were identified. High consistency patterns codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) insertions deletions (InDels) discovered across Variations presence pseudogene ycf1Ψ, resulting IR contraction expansion, reported. hyper-variable rpl16 was identified its exceptionally high Ka/Ks Pi values, implying that those frequent mutations occurred as result positive selection. Phylogenetic recovered based on full protein-coding genes. Overall, both sequences potential provided study enrich genomic Litsea. Valuable analysis also further research evolutionary patterns, markers, deeper
Language: Английский
Citations
27
Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)
Published: May 4, 2023
Abstract Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported size and gene contents plastomes, with little information on comparative analysis plastid genomes genus. Additionally, there are still some whose chloroplast genome has not been reported. In study, complete plastomes six were sequenced assembled, among them, P. campanulatum was for first time. Comparative phylogenetic analyses then conducted published three related species. Results indicated that whole plastome length ranged from 154,564 bp ( multiflorum ) 156,028 stenophyllum having a quadripartite structure LSC SSC separated by two IR regions. A total 113 unique genes detected each revealed content GC these highly identical. No significant contraction or expansion observed boundaries all except sibiricum 1, which rps19 pseudogenized owing incomplete duplication. Abundant long dispersed repeats SSRs genome. There five remarkably variable regions 14 positively selected identified Heteropolygonatum. Phylogenetic results based strongly supported placement alternate leaves sect. Verticillata , group characterized whorled leaves. Moreover, verticillatum cyrtonema displayed paraphyletic. This study characters Heteropolygonatum maintained high degree similarity. Five found be potential specific DNA barcodes . suggested leaf arrangement suitable basis delimitation subgeneric groups definitions require further study.
Language: Английский
Citations
14
International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(5), P. 2665 - 2665
Published: Feb. 25, 2024
is one of the largest genera and presents some most intricate taxonomic problems in family Orchidaceae, including species ornamental medical importance. The lack knowledge regarding characterization
Language: Английский
Citations
5
International Journal of Genomics, Journal Year: 2021, Volume and Issue: 2021, P. 1 - 15
Published: April 27, 2021
Chenopodium album sensu stricto belonging to C. aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed six chloroplast genomes s. str. collected in Korea understand relationship between and their morphological variations. All have a typical quadripartite structure with length ranging from 151,906 bp 152,199 bp, similar previously sequenced genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) 26 insertion deletion (INDEL) regions (308 total) were identified genomes, presenting low level intraspecific variations comparison other angiosperm species. 376 normal simple sequence repeats all seven genomes. The phylogenetic analysis based on available complete Amaranthaceae presents positions samples as well correlation one features. Our results provide way investigate features also insights understanding various characteristics including
Language: Английский
Citations
31
Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13
Published: Feb. 24, 2022
Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it protected at international and national levels. In this study, we sequenced its whole chloroplast genome for first time using next-generation sequencing (NGS) technology Illumina platform, performed comparative phylogenetic analysis related in Poaceae. The complete of C. 135,915 bp length, quadripartite structure having two 21,529 inverted repeat regions (IRs) dividing entire circular into large single copy region (LSC) 80,100 small (SSC) 12,757 bp. overall GC content 38.3%, while contents LSC, SSC, IR are 36.3%, 32.4%, 43.9%, respectively. A total 129 genes were annotated genome, including 83 protein-coding genes, 38 tRNA 8 rRNA genes. accD gene introns both clpP rpoC1 missing. addition, ycf1, ycf2, ycf15, ycf68 pseudogenes. Although was found to be conserved stable general, 26 SSRs 13 highly variable loci detected, these have potential developed important molecular markers subfamily Pooideae. Phylogenetic Poaceae indicated that Phippsia sister groups, provided new insights relationship between Coleanthus, Zingeria, Colpodium. This study presents initial report subtilis, provides essential data reference further research origin.
Language: Английский
Citations
20