The Nucleus, Journal Year: 2025, Volume and Issue: unknown
Published: April 29, 2025
Language: Английский
Plants, Journal Year: 2020, Volume and Issue: 9(6), P. 752 - 752
Published: June 15, 2020
Within the family Solanaceae, Withania is a small genus belonging to Solanoideae subfamily. Here, we report de novo assembled chloroplast genome sequences of W. coagulans, adpressa, and riebeckii. The length these genomes ranged from 154,162 154,364 base pairs (bp). These contained pair inverted repeats (IRa IRb) ranging 25,029 25,071 bp that were separated by large single-copy (LSC) region 85,635–85,765 (SSC) 18,457–18,469 bp. We analyzed structural organization, gene content order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide tandem repeats, substitutions plastomes, which revealed high similarities among species. Comparative analysis species also highlighted 10 divergent hotspots could potentially be used for molecular marker development, phylogenetic analysis, identification. Furthermore, our analyses showed even three mutational (rps4-trnT, trnM-atpE, rps15) sufficient discriminate included in current study.
Language: Английский
Citations
44
Genomics, Journal Year: 2020, Volume and Issue: 113(1), P. 183 - 192
Published: Dec. 15, 2020
Chloroplast (cp) genomes are considered important for the study of lineage-specific molecular evolution, population genetics, and phylogenetics. Our aim here was to elucidate evolution in cp species Dracunculus clade (Aroideae, Araceae). We report de novo assembled eight from genera also retrieved four National Center Biotechnology Information (NCBI). The varied size 162,424 bp 176,835 bp. Large Single Copy (LSC) region ranged 87,141 95,475 bp; Small (SSC) 14,338 23,981 Inverted Repeats (IRa IRb) 25,131 32,708 expansion inverted repeats led duplication ycf1 genes species. showed high similarity gene content yielded 113 unique (79 protein-coding, 4 rRNA, 30 tRNA genes). Codon usage, amino acid frequency, RNA editing sites, microsatellites repeats, transition transversion substitutions, synonymous non-synonymous substitutions were similar across clade. A previous reported deletion ycf1, accD, psbE, trnL-CAA, trnG-GCC Amorphophallus supports conservative structure including does not support mentioned above. suitable polymorphic loci based on comparative analyses species, which could be useful phylogenetic inference. Overall, current broad our knowledge about chloroplast genome aroids.
Language: Английский
Citations
41
Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)
Published: Nov. 13, 2020
Abstract Pulsatilla (Ranunculaceae) consists of about 40 species, and many them have horticultural and/or medicinal value. However, it is difficult to recognize identify wild species. Universal molecular markers been used these but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes seven The were very similar their length ranges from 161,501 162,669 bp. Eight highly variable regions potential sources such as simple sequence repeats, large repeat sequences, single nucleotide polymorphisms identified, which are valuable for studies infra- inter-specific genetic diversity. SNP number differentiating any two ranged 112 1214, provided sufficient data species delimitation. Phylogenetic trees based on different sets consistent with one another, IR, SSC barcode combination rbcL + matK trnH-psbA produced slightly results. relationships within certainly resolved using cp genome sequences. Overall, this study provides plentiful genomic resources, will be helpful members taxonomically challenging group in further investigation.
Language: Английский
Citations
40
Gene, Journal Year: 2021, Volume and Issue: 802, P. 145866 - 145866
Published: Aug. 3, 2021
Language: Английский
Citations
36
BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)
Published: March 19, 2022
Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species subfamily Aroideae phylogenetically perplexing due to shared interspecific morphological traits variation.This study, for first time ever, assembled analyzed complete chloroplast genomes of C. X. with genome sizes 165,906 bp, 153,149 bp 165,169 length, respectively. The were composed conserved quadripartite circular structures a total 131 annotated genes, including 8 rRNA, 37 tRNA 86 protein-coding genes. A comparison within showed seven genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 matK) linked environmental adaptation. Phylogenetic analysis confirmed close relationship gigantea esculenta S. colocasiifolia, sagittifolium. Furthermore, DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI trnS-trnG, psaC-ndhE trnS-trnG) harbored highly variable regions distinguish subfamily.These results would be beneficial identification, phylogenetic relationship, genetic diversity, potential germplasm resources Aroideae.
Language: Английский
Citations
26
Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 1002 - 1011
Published: Jan. 1, 2022
Amorphophallus konjac, a perennial herb in the Araceae family, is cash crop that can produce large amount of konjac glucomannan. To explore mechanisms underlying such genomes genus as well gene regulation glucomannan biosynthesis, we present chromosome-level genome assembly A. with total size 5.60 Gb and contig N50 1.20 Mb. Comparative genomic analysis reveals has undergone two whole-genome duplication (WGD) events quick succession. Two recent bursts transposable elements are identified genome, which contribute greatly to size. Our transcriptomic developmental corms characterizes key genes involved biosynthesis related starches. High expression cellulose synthase-like A, Cellulose D, mannan-synthesis 1, GDP-mannose pyrophosphorylase phosphomannomutase fructokinase contributes synthesis during corm expansion period while high starch synthase, branching enzyme phosphoglucomutase responsible for late development stage. In conclusion, generate high-quality different sequencing technologies. The caused this species. And provide valuable candidates molecular breeding future.
Language: Английский
Citations
24
Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13
Published: Sept. 15, 2022
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions exhibits a high degree of adaptability to different environments. At present, however, phylogenetic relationships this are not well resolved, chloroplast evolution remains poorly understood. Here, we sequenced, assembled, annotated genomes 10 species , downloaded assembled 13 additional based on next-generation sequencing data, compared them 46 previously published genomes. We found highly conserved genomic structure genus, with plastid genome sizes ranging from 159,929 bp ( langkokensis ) 160,657 religiosa ). Most chloroplasts encoded 113 unique genes, including set 78 protein-coding 30 transfer RNA (tRNA) four ribosomal (rRNA) one pseudogene infA The number simple sequence repeats (SSRs) ranged 67 sagittata 89 microdictya generally increased linearly size. Among plastomes, comparative analysis revealed eight intergenic spacers that were hotspot for divergence. Additionally, clpP rbcL ccsA genes showed evidence positive selection. Phylogenetic indicated none six traditionally recognized subgenera monophyletic. Divergence time complete sequences diverged rapidly during early middle Miocene. This research provides basic resources further evolutionary studies .
Language: Английский
Citations
24
Plants, Journal Year: 2020, Volume and Issue: 9(6), P. 737 - 737
Published: June 11, 2020
The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated genomes four genera representing three subfamilies Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), Orontium aquaticum (Orontioideae), performed comparative genomics using these genomes. sizes ranged from 163,770 bp to 169,982 bp. These comprise 113 unique genes, including 79 protein-coding, 4 rRNA, 30 tRNA genes. Among 17–18 genes are duplicated in inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 7 total number between 130 131. infA was found be a pseudogene all reported here. exhibited high similarities codon usage, amino acid frequency, RNA editing sites, microsatellites. oligonucleotide repeats junctions JSB (IRb/SSC) JSA (SSC/IRa) were highly variable among patterns IR contraction expansion shown homoplasious, therefore unsuitable for phylogenetic analyses. Signatures positive selection seen S. ycf2, clpP, rpl36. This study is valuable addition evolutionary history structure Araceae.
Language: Английский
Citations
39
BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)
Published: Oct. 2, 2021
Abstract Background As one of the largest genera in Apiaceae, Bupleurum L. is well known for its high medicinal value. The genus has frequently attracted attention evolutionary biologist and taxonomist distinctive characteristics Apiaceae family. Although some chloroplast genomes data have been now available, changes structure selective pressure not fully understood. In addition, few species are endemic to Southwest China, a distribution diversity center Chinese . Endemic key components biodiversity ecosystems, investigation features will be helpful develop better understanding process phylogeny genus. this study, we analyzed sequences whole 4 China comparison with published 17 determine phylogenetic relationships Asian Results complete genome 155,025 bp 155,323 length including SSC LSC region separated by pair IRs. Comparative analysis revealed an identical gene content across 21 species, total 114 unique genes (30 tRNA genes, rRNA 80 protein-coding genes). Chloroplast showed no rearrangements sequence identity (96.4–99.2%). They also shared similar tendency SDRs SSRs, but differed number (59–83). spite their conservation, they contained mutational hotspots, which can potentially exploited as high-resolution DNA barcodes discrimination. Selective that four were under positive selection. Phylogenetic formed two major clades, likely correspond geographical distribution. Conclusions provide important insights into evolution genu,
Language: Английский
Citations
29
Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 11
Published: Jan. 20, 2021
The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, chloroplast genomes. Correlations SNPs, InDels, have investigated the plant family Araceae previously using pair-wise sequence alignments of genomes two morphotypes one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), four species from Lemnoideae, a basal group. is large comprising 3,645 144 genera, grouped into eight subfamilies. In current study, we performed 34 comparisons 27 7 subfamilies determine correlation coefficients mutational events at family, subfamily, genus levels. We express strength correlations as: negligible or very weak (0.10–0.19), (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), (0.70–0.99), perfect (1.00). observed strong/very most comparisons, whereas few showed correlations. average coefficient was recorded as 0.66 between “SNPs InDels,” 0.50 “InDels repeats,” 0.42 repeats.” qualitative analyses, 95–100% sub-family level, while 36–86% level co-occurred with SNPs same bins. Our findings show that such exist throughout support hypothesis distribution proxy for hotspots.
Language: Английский
Citations
28