Comparative chloroplast genomics of Caryophyllaceae species: insights into sequence variations and phylogenetic evolution DOI Creative Commons
Lucun Yang,

Yongqing Zhu,

Qing Hua

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Dec. 27, 2024

Caryophyllaceae contains 100 genera and 3000 species, many of which are valuable both ecologically economically. However, as past research has shown, the fundamental phylogenetic relationships still debatable, molecular dating based on chloroplast genomes not been thoroughly examined for entire family. In this study, complete genome sequences Arenaria kansuensis Maxim., A. roborowskii przewalskii Silene aprica Turcz were described. Additionally, four newly generated along with eighteen published included comparative genomics analysis. These 22 had typical quadripartite structure, 128–134 distinct genes lengths ranging from 133,621 bp to 153,957 bp. The showed significant variations in number long repeats SSR types; mononucleotide (A/T) palindromic most common types. Three substantially divergent areas containing atpB-rbcL, rbcL-accD, accD found by further could serve effective markers. codon bias mainly affected natural selection, but other factors such mutation pressure also affect some extent. Fourteen optimal codons identified Caryophyllaceae. Phylogenetic analysis demonstrated that monophyly any three recognized subfamilies within was supported our data. Meanwhile, seven well-supported clades correspond 8 tribes trees. results divergence between Amaranthaceae estimated occur 69 Ma. Paronychieae oldest tribe eight diverged at 59.92 This study provides resources investigations identification, genetic engineering, evolution, phylogeny species.

Language: Английский

Unveiling the conserved nature of Heliconia chloroplast genomes: insights from the assembly and analysis of four complete chloroplast genomes DOI Creative Commons
Xin Cheng, Chengcheng Shi, Ting Yang

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 16, 2025

Heliconia, a genus within the Zingiberales order, is renowned for its diverse morphology, suggesting rich genetic reservoir. However, research on plants Heliconiaceae family has primarily focused taxonomy and phylogenetics, with limited exploration into other aspects, particularly chloroplast genome. Given significance of genomes in evolutionary studies, deeper understanding their structure diversity Heliconia essential. In this study, we sequenced assembled complete four representative species: bihai, caribaea, orthotricha, tortuosa. The were analyzed structure, gene content, nucleotide diversity. We also performed comparative analysis species order to investigate structural functional differences. exhibited typical quadripartite ranged length from 161,680 bp 161,913 bp. All contained 86 protein-coding genes. Comparative revealed that genome structures different highly conserved, minor variations. Notably, was slightly shorter than those species, due reduced inverted repeat region. terms diversity, lower compared families order. This study provides valuable insights conserved nature Heliconia. size, shortened region, marks distinct feature family. Our findings underscore low which could be indicative history differentiation. These results contribute broader evolution offer important resources future related species.

Language: Английский

Citations

1
Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema DOI Creative Commons
Dongmei Li,

Yan-Gu Pan,

X. J. Wu

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: May 23, 2024

Abstract Aglaonema commutatum is a famous species in the genus, which has important ornamental and economic value. However, its chloroplast genome information phylogenetic relationships among popular green cultivars of southern China have not been reported. Herein, genomes one variety A. seven , namely, ‘San Remo’, ‘Kai Sa’, ‘Pattaya Beauty’, ‘Sapphire’, ‘Silver Queen’, ‘Snow White’, ‘White Gem’, Horse Prince’, were sequenced assembled for comparative analysis phylogeny. These eight possessed typical quadripartite structure that consisted LSC region (90,799–91,486 bp), an SSC (20,508–21,137 bp) pair IR regions (26,661–26,750 bp). Each contained 112 different genes, comprising 79 protein-coding 29 tRNA genes 4 rRNA genes. The gene orders, GC contents, codon usage frequency, IR/SC boundaries highly conserved these genomes. Long repeats, SSRs, SNPs indels analyzed Comparative 15 identified 7 variable regions, including trnH-GUG-exon1-psbA trnS-GCU-trnG-UCC-exon1 trnY-GUA-trnE-UUC psbC-trnS-UGA trnF-GAA-ndhJ ccsA-ndhD rps15-ycf1-D2 . Reconstruction trees based on genomes, strongly supported was sister to Anchomanes genus classified into two clades clade I II, corresponded sections, Chamaecaulon respectively. One five cultivars, I; rest ‘Sapphire’ II. Positive selection observed 34 at level amino acid sites 77 Araceae family Based DNA markers developed differentiate II In conclusion, this study provided genomic resources useful classification

Language: Английский

Citations

1
Comparative Analysis of the Chloroplast Genomes of the Melliodendron (Styracaceae) Species: Providing Insights into Molecular Evolution and Phylogenetic Relationships DOI Open Access

Wei Dai,

Hao-Zhi Zheng, Menghan Xu

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 26(1), P. 177 - 177

Published: Dec. 28, 2024

Melliodendron xylocarpum is a member of the Styracaceae family, which well-known for its remarkable ornamental and medicinal properties. In this research, we conducted comparative analysis chloroplast genomes from four samples M. xylocarpum, representing Melliodendron. The results demonstrated that genome ranging 157,103 bp to 158,357 exhibited typical quadripartite structure, including one large single-copy (LSC) region (90,131 90,342 bp), small (SSC) (18,467 18,785 two inverted repeat regions (IRs) (24,115 24,261 bp). Different levels expansion contraction were observed in IR samples. Besides, accD ycf1 have been identified under positive selection, potentially linked adaptive response various environmental changes. Conflicting phylogenetic relationships among genera within family tree constructed using CDS sequences complete genomes. Furthermore, significance sample size was also highlighted study enhancing accuracy findings analyses. research will provide significant insights future investigations into evolutionary trends conservation species.

Language: Английский

Citations

1
Asymmetric distribution of mineral nutrients aggravates uneven fruit pigmentation driven by sunlight exposure in litchi DOI

Xuexia Su,

Xiaotong Zhang,

Cuihua Bai

et al.

Planta, Journal Year: 2023, Volume and Issue: 258(5)

Published: Oct. 11, 2023

Language: Английский

Citations

2
Comparative chloroplast genomics of Caryophyllaceae species: Insights into sequence variations and phylogenetic evolution DOI Creative Commons
Lucun Yang,

Yongqing Zhu,

Qing Hua

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 12, 2024

Abstract Background Caryophyllaceae contains 100 genera and 3000 species, many of which are valuable both ecologically economically. However, as past research has shown, the fundamental phylogenetic relationships still debatable, molecular dating based on chloroplast genomes not been thoroughly examined for entire family. Methods In this study, we used four newly generated eighteen other published to clarify their genetic properties. Results These 22 had typical quadripartite structure, with 129–134 distinct genes lengths ranging from 133,621 bp 153,957 bp. The showed significant variations in number long repeats SSR types; mononucleotide (A/T) palindromic were most common types. Three substantially divergent areas containing atpB - rbcL , accD found by further comparative could serve effective markers. codon bias mainly affected natural selection, but factors such mutation pressure also affect some extent. Fourteen optimal codons identified genome Caryophyllidae. Phylogenetic analysis demonstrated that monophyly any three recognized subfamilies within was supported our data. Meanwhile, seven well-supported clades correspond 8 tribes trees. results divergence between Amaranthaceae estimated occur 69 Ma. Tr. Paronychieae oldest tribe eight included diverged at 59.92 Conclusion This study provides resources investigations identification, engineering, evolution, phylogeny species.

Language: Английский

Citations

0
Comparative analysis of the complete chloroplast genomes of thirteen Bougainvillea cultivars from South China with implications for their genome structures and phylogenetic relationships DOI Creative Commons

X. J. Wu,

H.B. Wang,

Shui-Ping Zou

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(9), P. e0310091 - e0310091

Published: Sept. 11, 2024

Bougainvillea spp., belonging to the Nyctaginaceae family, have high economic and horticultural value in South China. Despite similarity terms of leaf appearance hybridization among species, especially × buttiana , their phylogenetic relationships are very complicated controversial. In this study, we sequenced, assembled analyzed thirteen complete chloroplast genomes cultivars from China, including ten B . three other cultivars, identified within genus species family for first time. These 13 had typical quadripartite structures, comprising a large single-copy (LSC) region (85,169–85,695 bp), small (SSC) (18,050–21,789 pair inverted-repeat (IR) regions (25,377–25,426 bp). each contained 112 different genes, 79 protein-coding 29 tRNAs 4 rRNAs. The gene content, codon usage, simple sequence repeats (SSRs), long were essentially conserved these genomes. Single-nucleotide polymorphisms (SNPs) insertions/deletions (indels) detected Four divergent regions, namely, trnH-GUG_psbA trnS-GCU_trnG-UCC-exon1 trnS-GGA_rps4 ccsA_ndhD comparative analysis 16 cultivar Among 46 nine rps12 rbcL ndhF rpoB rpoC2 ndhI psbT ycf2 ycf3 found be under positive selection at amino acid site level. Phylogenetic based on genes revealed that was sister Belemia with strong support 35 individuals divided into strongly supported clades, Clades Ⅰ, Ⅱ, Ⅲ Ⅳ. Clade Ⅰ included 6 individuals, which 2 ‘Gautama’s Red’ spectabilis ‘Flame’. Ⅱ only spinosa comprised 7 wild species. Ⅳ 21 11 ‘Mahara’, ‘California Gold’, ‘Double Salmon’, Yellow’, ‘Los Banos Beauty’, ‘Big Chitra’, ‘San Diego Red’, ‘Barbara Karst’, glabra ‘ White Stripe’, ‘Splendens’ ‘Miss Manila’ sp. 1. conclusion, study not provided valuable genome resources but also helped identify understand evolution family.

Language: Английский

Citations

0
Comparative chloroplast genomics of Caryophyllaceae species: insights into sequence variations and phylogenetic evolution DOI Creative Commons
Lucun Yang,

Yongqing Zhu,

Qing Hua

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Dec. 27, 2024

Caryophyllaceae contains 100 genera and 3000 species, many of which are valuable both ecologically economically. However, as past research has shown, the fundamental phylogenetic relationships still debatable, molecular dating based on chloroplast genomes not been thoroughly examined for entire family. In this study, complete genome sequences Arenaria kansuensis Maxim., A. roborowskii przewalskii Silene aprica Turcz were described. Additionally, four newly generated along with eighteen published included comparative genomics analysis. These 22 had typical quadripartite structure, 128–134 distinct genes lengths ranging from 133,621 bp to 153,957 bp. The showed significant variations in number long repeats SSR types; mononucleotide (A/T) palindromic most common types. Three substantially divergent areas containing atpB-rbcL, rbcL-accD, accD found by further could serve effective markers. codon bias mainly affected natural selection, but other factors such mutation pressure also affect some extent. Fourteen optimal codons identified Caryophyllaceae. Phylogenetic analysis demonstrated that monophyly any three recognized subfamilies within was supported our data. Meanwhile, seven well-supported clades correspond 8 tribes trees. results divergence between Amaranthaceae estimated occur 69 Ma. Paronychieae oldest tribe eight diverged at 59.92 This study provides resources investigations identification, genetic engineering, evolution, phylogeny species.

Language: Английский

Citations

0