Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Genomics, Journal Year: 2019, Volume and Issue: 112(1), P. 581 - 591

Published: April 15, 2019

Language: Английский

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Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae

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

Published: Feb. 5, 2025

Language: Английский

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Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

BMC Plant Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Sept. 2, 2020

Abstract Background Oat ( Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences eleven species, to examine plastome evolutionary dynamics analyze phylogenetic relationships between oat congeneric wild related species. Results The genomes (size range 135,889–135,998 bp) share quadripartite structure, comprising large single copy (LSC; 80,014–80,132 bp), small (SSC; 12,575–12,679 pair inverted repeats (IRs; 21,603–21,614 bp). plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs 39 transfer RNAs. nucleotide sequence diversities (Pi values) from 0.0036 rps19 ) 0.0093 rpl32 for ten most polymorphic 0.0084 psbH-petB 0.0240 petG-trnW-CCA intergenic regions. Gene selective pressure analysis shows that all have been under purifying selection. adjacent position tandem repeats, insertions/deletions polymorphisms support importance in causing mutations . Phylogenomic analyses, based on complete LSC intermolecular recombination sequences, monophyly with two clades genus. Conclusions Diversification explained by presence highly diverse regions, recombination, co-occurrence repeat indels or polymorphisms. study demonstrates diploid-polyploid lineage maintains subclades derived maternal ancestors, A. longiglumis as first diverging clade I. These resources will be helpful elucidating understanding at genus family Poaceae levels, are potentially useful exploit variation making hybrids plant breeding.

Language: Английский

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Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Jan. 26, 2023

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one the most diverse genera angiosperms, Carex is great value for study evolutionary relationships speciation within its genus, but limited due to highly expanded restructured with large number repeats. In this study, we provided more detailed account using hybrid assembly second- third-generation sequencing examined structural variation genus. revealed four species are significantly longer than characterized by sequence rearrangement rates, low GC content density, increased repetitive sequences. location studied closely related positions long repeat sequences; genus provides typical example expansion caused Phylogenetic constructed based on protein-coding genes support latest taxonomic system Carex, while revealing may some phylogenetic significance. Moreover, demonstrated approach short reads analyze complex also an important reference analysis rearrangements other taxa.

Language: Английский

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Correlations among oligonucleotide repeats, nucleotide substitutions, and insertion–deletion mutations in chloroplast genomes of plant family Malvaceae

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 59(2), P. 388 - 402

Published: March 19, 2020

Abstract The co‐occurrence of mutational events including substitutions and insertions–deletions (InDels) with oligonucleotide repeats has previously been reported for a limited number prokaryotic, eukaryotic, organelle genomes. In this study, the correlations among these in chloroplast genomes species eudicot family Malvaceae were investigated. This study also genome sequences Hibiscus mutabilis , Malva parviflora Malvastrum coromandelianum . These three 16 other publicly available from 12 genera used to calculate correlation coefficients at family, subfamily, genus levels. comparisons, pairwise aligned record InDels mutually exclusive, 250 nucleotide long bins. Taking one two as reference, coordinate positions reference recorded. extent repeats, substitutions, was calculated categorized follows: very weak (0.1–0.19), (0.20–0.29), moderate (0.30–0.39), strong (0.4–0.69). ranged 0.201–0.6 between “InDels single‐nucleotide polymorphism (SNP)”, 0.182–0.513 repeat” 0.055–0.403 “SNPs repeats”. At family‐ subfamily‐level 88%–96% showed SNPs, whereas level, 23%–86% co‐occurred SNPs same Our findings support previous hypothesis suggesting use proxy finding hotspots.

Language: Английский

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Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

Journal of Molecular Evolution, Journal Year: 2020, Volume and Issue: 88(7), P. 562 - 574

Published: July 9, 2020

Abstract The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report chloroplast genomes of two species Pothoideae: Anthurium huixtlense (size: 163,116 bp) and Pothos scandens 164,719 bp). genome P. showed unique contraction expansion inverted repeats (IRs), thereby increasing size large single-copy region (LSC: 102,956 decreasing small (SSC: 6779 This led duplication many genes due transfer IR regions from (SSC) region, whereas some duplicate became single copy regions. rate evolution protein-coding was affected by IRs; found higher mutation rates for that exist in as compared those IRs. We a 2.3-fold increase oligonucleotide when with A. , amino acid frequency codon usage revealed similarities. ratio transition transversion mutations 2.26 2.12 . Transversion mostly translated non-synonymous substitutions. phylogenetic inference limited monophyly Araceae subfamilies. Our study provides insight into molecular

Language: Английский

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Plastid genomics ofNicotiana(Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

PeerJ, Journal Year: 2020, Volume and Issue: 8, P. e9552 - e9552

Published: July 23, 2020

Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated non-food crops and garden ornamentals. In addition worldwide production leaves, they also used evolutionary model systems due their complex development history tangled by polyploidy hybridization. Here, we assembled plastid genomes five species: N. knightiana, rustica, paniculata, obtusifolia glauca . De novo had typical quadripartite structure, consisting a pair inverted repeat (IR) regions (25,323–25,369 bp each) separated large single-copy (LSC) region (86,510–86,716 bp) small (SSC) (18,441–18,555 bp). Comparative analyses with currently available Solanaceae genome sequences showed similar GC gene content, codon usage, simple sequence oligonucleotide repeats, RNA editing sites, substitutions. We identified 20 highly polymorphic regions, mostly belonging intergenic spacer (IGS), which could be suitable for robust cost-effective markers inferring phylogeny family Solanaceae. Our comparative analysis revealed that maternal parent tetraploid rustica was common ancestor paniculata knightiana , later species is more closely related Relaxed molecular clock estimated speciation event between appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical supported south-to-north range expansion diversification species, where undulata evolved in North/Central Peru, while developed Southern Peru from adapted coastal climatic regimes. further inspected selective pressure on protein-coding genes among determine if this adaptation process affected evolution genes. These indicate four involved different functions, including DNA replication ( rpo A) photosynthesis atp B, ndh D ndhF ), came under positive result specific environmental conditions. Genetic mutations these might have contributed better survival superior adaptations during species.

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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Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

BMC Plant Biology, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 23, 2021

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in each possess 50 or more species, including Globba (100), Hedychium ( > 80), Kaempferia (50) Zingiber (150). Despite agricultural, medicinal horticultural importance these genomic resources suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled analyzed ten complete chloroplast genomes from nine species Zingiberoideae: lancangensis , marantina multiflora schomburgkii var. angustata coccineum neocarneum rotunda ‘Red Leaf’, ‘Silver Diamonds’ recurvatum . These (size range 162,630–163,968 bp) typical quadripartite structures that consist single copy (LSC, 87,172–88,632 bp), small (SSC, 15,393–15,917 pair inverted repeats (IRs, 29,673–29,833 bp). The contain 111–113 different genes, 79 protein coding 28–30 tRNAs 4 rRNA genes. dynamics genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long exhibit similarities, with slight differences observed among genomes. Further comparative analysis seventeen related 12 divergent hotspots identified. Positive selection 14 accD ccsA ndhA ndhB psbJ rbcL rpl20 rpoC1 rpoC2 rps12 rps18 ycf1 ycf2 ycf4. Phylogenetic analyses, based on chloroplast-derived single-nucleotide polymorphism data, strongly support Curcuma I + “ clade” consisting II, form nested evolutionary relationship Zingiberoideae. Conclusions Our study provides detailed information genomes, representing valuable resource future studies seek to understand identified can be used development phylogenetic inference identification closely within four

Language: Английский

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Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

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

Published: Jan. 17, 2024

Abstract Background Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in tropical regions South America, Africa, and Southeast Asia, which some have important ornamental, medicinal ecological values. Previous studies on phylogenetic taxonomic Costaceae by using nuclear internal transcribed spacer ( ITS ) chloroplast genome fragments data had low resolutions. Additionally, structures, variations molecular evolution complete genomes still remain unclear. Herein, a total 13 including 8 newly sequenced 5 from NCBI GenBank database, representing all three distribution this were comprehensively analyzed for comparative genomics relationships. Result The possessed typical quadripartite structures with lengths 166,360 to 168,966 bp, comprising large single copy (LSC, 90,802 − 92,189 bp), small (SSC, 18,363 20,124 bp) pair inverted repeats (IRs, 27,982 29,203 bp). These coded 111 113 different genes, 79 protein-coding 4 rRNA genes 28 30 tRNAs genes. gene orders, contents, amino acid frequencies codon usage within highly conservative, but several intron loss, long repeats, simple sequence (SSRs) expansion IR/SC boundaries also found among these genomes. Comparative identified five divergent ndhF, ycf1-D2 , ccsA-ndhD rps15-ycf1-D2 rpl16-exon2-rpl16-exon1 . Five combined DNA + ndhF could be used potential markers future analyses identification Costaceae. Positive selection was eight cemA, clpP ndhA petB psbD rps12 ycf1 Maximum likelihood Bayesian trees sequences consistently revealed identical tree topologies high supports between Three clades divided Asian clade, Costus clade American clade. Tapeinochilos sister Hellenia Parahellenia cluster strong support results dating showed that crown age about 30.5 Mya (95% HPD: 14.9 49.3 Mya), then started diverge into around 23.8 10.1 41.5 Mya). diverged at 10.7 3.5 25.1 Conclusion can resolve relationships provide new insights evolution. would useful inference

Language: Английский

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