CPJSdraw: analysis and visualization of junction sites of chloroplast genomes

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e15326 - e15326

Published: May 10, 2023

Background Chloroplast genomes are usually circular molecules, and most of them tetrad structures with two inverted repeat (IR) regions, a large single-copy region, small region. IR contraction expansion among the genetic diversities during evolution plant chloroplast genomes. The only previously released tool for visualization junction sites regions does not consider diversity starting point genomes, which leads to incorrect results or even no examination expansion. Results In this work, new named CPJSdraw was developed visualizing can format irregular linearized genome, correct display structure, visualize any number (≥1) show transcription direction genes adjacent sites, indicate Conclusions is software that universal reliable in analysis has more accurate complete functions when compared tool. as perl package tested data available at http://dx.doi.org/10.5281/zenodo.7669480 English users. addition, an online version Chinese interface http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335 .

Language: Английский

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A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 2, 2025

Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible functional foods. In this study, we compared plastid genomes (plastomes) 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that accessions were monophyletic within genus Peucedanum. However, ten plastomes classified into two different groups according to their length inverted repeat (IR) block, short-type (S-type) plastome group containing 18.6 kbp original IR long-type (L-type) 35.7 expanded by duplication 17.1 large single copy region. A total nine nucleotide polymorphisms eight insertions or deletions identified among five L-type plastomes, whereas variations S-type plastomes. Calculation synonymous substitution rates divergence time estimation suggested 17 expansion occurred recently. Molecular markers developed validated classify 55 germplasm types. Our study would be useful unraveling dynamic evolution family molecular breeding PJ.

Language: Английский

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Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(12), P. 7810 - 7826

Published: May 6, 2021

Abstract The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues the phylogeny of due low polymorphism molecular markers. Therefore, suitable polymorphic regions need be identified. Here, we de novo assembled plastomes three species B . oxyodonta , B. tenella balsamifera compared them with 26 other Asteroideae after correction annotations. These quadripartite similar gene content, genome organization, inverted repeat contraction expansion comprising 113 genes, 80 protein‐coding, 29 transfer RNA, 4 ribosomal RNA genes. comparative analysis codon usage, amino acid frequency, microsatellite repeats, oligonucleotide transition transversion substitutions has revealed high resemblance among newly We identified 10 highly nucleotide diversity above 0.02, rps 16‐ trn Q, ycf 1, ndh F‐ rpl 32, pet N‐ psb M, 32‐ L, they may for development robust, authentic, cost‐effective markers barcoding inference Among these regions, five also co‐occurred repeats support use as a proxy identification loci. phylogenetic close relationship between Pluchea within tribe Inuleae. At level, our supports sister Astereae Anthemideae rooted Gnaphalieae, Calenduleae, Senecioneae. results are contradictory recent which reported “Senecioneae Anthemideae” “Astereae Gnaphalieae” or Gnaphalieae Anthemideae, then Senecioneae using nuclear sequences. conflicting signals observed at tribal level plastidt data require further investigation.

Language: Английский

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Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: Feb. 26, 2022

Abstract Background The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists 10 tribes, > 90 genera, 2000 species. Previous molecular phylogenetics using limited numbers markers were often unable to fully resolve the phylogenetic relationships at tribal generic levels. Also, structural variations plastomes (PSVs) within tribes have been poorly investigated in previous studies. To understand PSVs clade, highly reliable sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 (40 newly sequenced assembled rest from GenBank) comparatively analyzed decipher four data matrices. Results All are typically quadripartite size ranging 153,055 155,908 bp contained 111 unique genes. inverted repeat (IR) regions experienced multiple contraction expansion; five types detected but most abundant was SSR. its elements affected by IR boundary shifts types. However, emerging had no taxonomic implications. Eight divergent identified plastome ndhF, ccsA, ndhD, ndhA, ndhH, ycf1 , rps16-trnQ-UUG, psbM-trnD . These variable may be potential for further species delimitation population genetic analyses clade. Our phylogenomic yielded a well-resolved phylogeny tree well-support levels alliance. Conclusions Plastome could indispensable resolving tribes. Therefore, study provides deep insights into Rubiaceae family as whole.

Language: Английский

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Chloroplast genome evolution in the Dracunculus clade (Aroideae, Araceae)

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

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Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

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

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Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 11

Published: Feb. 11, 2021

In this study, we assembled and annotated the chloroplast (cp) genome of Euonymus species fortunei , phellomanus maackii performed a series analyses to investigate gene structure, GC content, sequence alignment, nucleic acid diversity, with objectives identifying positive selection genes understanding evolutionary relationships. The results indicated that cp was 156,860–157,611bp in length exhibited typical circular tetrad structure. Similar majority angiosperm genomes, yielded large single-copy region (LSC) (85,826–86,299bp) small (SSC) (18,319–18,536bp), separated by pair sequences (IRA IRB; 26,341–26,700bp) same encoding but opposite directions. 130–131 genes, including 85–86 protein coding 37 tRNA eight rRNA contents 37.26–37.31%. content variable among regions highest inverted repeat (IR) region. IR boundary happened expanding resulting rps19 entered into doubled completely. Such fluctuations at border positions might be helpful determining relationships . simple-sequence repeats (SSRs) were composed primarily single nucleotides (A)n (T)n, mostly 10–12bp length, an obvious A/T bias. We identified several loci suitable polymorphism potential use as molecular markers for inferring phylogeny within genus Signatures seen rpoB genes. Based on data from whole genome, common copy LSC, SSC, regions, constructed tree related species, which consistent traditional taxonomic classifications. It showed E. sister japonicus whereby appeared hamiltonianus Our study provides important genetic information support further investigations phylogenetic development adaptive evolution species.

Language: Английский

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Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

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

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The complete chloroplast genome sequence of Amorphophallus konjac (Araceae) from Yunnan, China and its phylogenetic analysis in the family Araceae

Mitochondrial DNA Part B, Journal Year: 2024, Volume and Issue: 9(1), P. 41 - 45

Published: Jan. 2, 2024

This work determined and analyzed the complete chloroplast genome sequence of Amorphophallus konjac K. Koch ex N.E.Br 1858 from Yunnan, China. The size was 167,470 bp, which contains a large single-copy region (LSC 93,443 bp), small (SSC 21,575 pair inverted repeat regions (IR 26,226 bp). has 131 genes, including 86 protein-coding 37 tRNAs, eight rRNAs. A previous study reported deletion accD, psbE, trnG-GCC genes in A. genome. Our supports conservative structure does not support gene mentioned above. Phylogenetic analysis indicated that shares close relationship with another (collected Guizhou) titanium by forming clade genus Amorphophallus. results provide some useful information to evolution family Araceae.

Language: Английский

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Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae)

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: March 5, 2024

Abstract Background Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing disjunct distribution worldwide across all the continents except Antarctica. There are numerous that commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., Southern Hemisphere clade. However, relationships clades differ greatly between nuclear plastid topologies. has been limited exploration chloroplast phylogenetic within Ampelopsideae, studies on genome structure this only available for few individuals. In study, we aimed to investigate evolutionary characteristics genomes tribe, their insights. Results We sequenced, assembled, annotated 36 related taxa in family. Three main were corresponding , lineage, respectively, 100% bootstrap supports. sequences content highly conserved. comparative analyses suggested plastomes demonstrate contraction large single copy region an expansion inverted repeat region, possess high number forward palindromic distinct both taxa. Conclusions Our results highlighted plastome variations length, or codon usage bias, sequences, lineages which probably faced different environmental selection pressures history. This study provides valuable insights understanding patterns Vitaceae.

Language: Английский

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