Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

Plants, Journal Year: 2024, Volume and Issue: 13(10), P. 1332 - 1332

Published: May 12, 2024

The family Chenopodiaceae Vent. (Amaranthaceae

Language: Английский

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Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

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

Published: May 9, 2023

Trichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified phylogenetic relationships within this on several DNA markers, including generic subtribes. Recently, plastid phylogenomics been successfully employed resolve at different taxonomic levels. In study, were used explore Trichosporeae. Eleven plastomes Hemiboea newly reported. Comparative analyses, phylogeny morphological character evolution conducted 79 species representing seven The range from 152,742 bp 153,695 in length. Within Trichosporeae, sampled 152,196 156,614 GC content 37.2% 37.8%. A total 121-133 genes annotated each species, 80-91 protein-coding genes, 34-37 tRNA 8 rRNA genes. contraction expansion IR borders detected, gene rearrangements inversions did occur. 13 hypervariable regions proposed as potential molecular markers for identification. 24,299 SNPs 3,378 indels inferred, functionally missense silent variations. There 1968 SSRs, 2055 tandem repeats 2802 dispersed repeats. RSCU ENC values indicated that codon usage pattern was conserved Both frameworks based whole plastome 80 CDSs basically concordant. sister between Loxocarpinae Didymocarpinae confirmed, Oreocharis a group with high support. characters showed complex evolutionary Our findings may contribute future research genetic diversity, patterns, conservation

Language: Английский

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Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: March 13, 2024

This study presents a comprehensive analysis of the chloroplast (cp) genomes Cornus species, including comparative and phylogenetic evaluations, as well examinations their genomic structure composition. The cp exhibit typical circular quadripartite demonstrate highly similar gene order structure. complete genome size 10 taxa in this is 156,965 bp to 157,383 bp, where length large single-copy (LSC) region 86,296 86,691 small (SSC) 18,386 18,454 inverted repeat (IR) 23,143 26,112 bp. A total 131 genes were found, 86 protein-coding (PCGs), eight rRNA genes, 37 tRNA genes. mean GC content 38.145%, LSC 36.396%, SSC 32.372%, IR 43.076%. Despite relatively conserved nature within species , 25–31 simple sequence repeats (SSRs) identified our study. SSRs found be distributed LSC, SSC, regions hongkongensis subsp. C. elegans gigantea tonkinensis while SSR was not other six taxa. Thus, whole genomics valuable tool for identification, taxonomic clarification, evolutionary analysis. Furthermore, findings reveal that along with kousa elliptica form sister groups. Notably, ferruginea melanotricha did affinity . Our furnishes essential data further research on classification provides novel insights into relationship subg. Syncarpea

Language: Английский

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Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Forests, Journal Year: 2022, Volume and Issue: 13(2), P. 265 - 265

Published: Feb. 8, 2022

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It an important ornamental and potential medicinal plant resource. Here, we assembled annotated the chloroplast (cp) genome of E. maackii. By combining this with seven available cp genomes from species, performed plastome variation analysis Euonymus. Furthermore, reconstructed phylogenetic estimated differentiation time The newly was 157,551 bp in size had typical quadripartite structure, which consisted one large single-copy (LSC 86,524 bp) region, (SSC 18,337 pair inverted repeat regions (26,345 bp). A total 652 single nucleotide polymorphisms (SNPs) 65 insertions/deletions (indels) were detected between two maackii, overall genetic 4.1 SNPs per kb or π value 0.00443, reflecting high level intraspecific variation. Some coding noncoding higher identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, psbC-trnS-UGA. hypervariable not same as those divergence based on whole showed that species formed clade, sister Catha edulis Maytenus guangxiensis, they separated 24.74 million years ago. hamiltonianus most closely related, having each other only approximately 2.68 Our study provides information for further studies such its phylogeography, population genetics molecular ecology, new insights into evolution

Language: Английский

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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests, Journal Year: 2021, Volume and Issue: 12(7), P. 861 - 861

Published: June 29, 2021

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species genus Castanea (chestnuts chinquapins) valued as a source nuts timber wherever they grow, chestnut hybrids common. We compared cp C. mollissima, seguinii, henryi, pumila. These ranged from 160,805 bp to 161,010 length, comprising pair inverted repeat (IR) regions (25,685 25,701 bp) separated by large single-copy (LSC) region (90,440 90,560 small (SSC) (18,970 19,049 bp). Each genome encoded same 113 genes; 82–83 protein-coding genes, 30 transfer RNA four ribosomal genes. There were 18 duplicated genes IRs. Comparative analysis revealed that rpl22 was absent all analyzed species, gene ycf1 has been pseudo-genized Chinese chestnuts except pumlia. repeats nucleotide substitutions these plastomes detected several highly variable regions. The analyses based on confirmed monophyly species.

Language: Английский

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The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships

Genes, Journal Year: 2023, Volume and Issue: 14(1), P. 227 - 227

Published: Jan. 15, 2023

Ophiorrhiza baviensis Drake, a flowering medical plant in the Rubiaceae, exists uncertainly within genus’ evolutionary relationships. For first time, whole chloroplast (cp) genome of an O. Drake species was sequenced and annotated. Our findings demonstrate that complete cp is 154,770 bp size, encoding total 128 genes, including 87 protein-coding 8 rRNAs, 33 tRNAs. A 59 SSRs were screened studied genome, along with six highly variable loci, which can be applied to generate significant molecular markers for genus. The comparative analysis two published others genus revealed high similarity; however, there some notable gene rearrangements densa plastome. maximum likelihood phylogenetic trees constructed based on concatenation rps16 trnL-trnF intergenic spacer sequence, indicating close relationship between other Ophiorrhiza. This study will provide theoretical basis identifying as well genus, contribute shedding light evolution Rubiaceae.

Language: Английский

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Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae)

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: July 14, 2023

Lysimachia L., the second largest genus within subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is diversity center Lysimachia, containing 150 species. Despite advances in backbone phylogeny species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 We aimed identify plastome structure features and hypervariable loci Lysimachia. Additionally, phylogenetic conflict signals were examined.These fifty had typical quadripartite structure, with lengths varying from 152,691 155,784 bp. Plastome size was positively correlated IR intron length. Thirteen highly variable regions identified. ndhB, petB ycf2 found be under positive selection. Plastid ML trees tree strongly supported that L. maritima as sister subg. Palladia + (Christinae clade), while nrDNA clearly placed a group.The structures these generally conserved, but potential plastid markers signatures selection detected. These data provided new insights into interspecific including cytonuclear discordance position maritima, which may result ghost introgression past. Our findings have established basis further exploration taxonomy, evolutionary history

Language: Английский

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Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Dec. 5, 2023

Abstract Background Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources P. are scarce, a clear phylogenetic evolutionary history this species yet to be elucidated. Here, we sequenced analyzed complete chloroplast genome of compared it with related genus based on genome. Results The 157,935 bp long typical tetrad structure, overall GC content 36.72% higher inverted repeats (IR) regions than large single-copy (LSC) small (SSC) regions. It contains 130 genes, including 85 protein-coding 37 tRNA 8 rRNA genes. ycf3 clpP genes have two introns, longest intron trnK-UUU gene LSC region. Moreover, total 253SSRs, mononucleotide SSRs being most abundant. sequences arrangements highly conserved, structure order similar other species. atpE , ccsA petA rps8 matK undergone significant positive selection close relationship jamasakura . coding IR more conserved noncoding regions, DNA throughout Conclusions current genomic datasets provide valuable information further identification, evolution, research

Language: Английский

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Comparison of Boraginales Plastomes: Insights into Codon Usage Bias, Adaptive Evolution, and Phylogenetic Relationships

Diversity, Journal Year: 2022, Volume and Issue: 14(12), P. 1104 - 1104

Published: Dec. 12, 2022

The Boraginales (Boraginaceae a.l.) comprise more than 2450 species worldwide. However, little knowledge exists of the characteristics complete plastid genome. In this study, three new sequences representing first pt genome Heliotropiaceae and Cordiaceae were assembled compared with other species. sizes Cordia dichotoma, Heliotropium arborescens, Tournefortia montana 151,990 bp, 156,243 155,891 respectively. Multiple optimal codons identified, which may provide meaningful information for enhancing gene expression Furthermore, codon usage bias analyses revealed that natural selection factors dominate patterns in boundaries IR/LSC IR/SSC regions significantly different, we also found a signal obvious IR region expansion Nonea vesicaria Arnebia euchroma. Genes high nucleic acid diversity (pi) values calculated, be used as potential DNA barcodes to investigate phylogenetic relationships Boraginales. psaI, rpl33, rpl36, rps19 under positive selection, these genes play an important role our understanding adaptive evolution Phylogenetic implied can divided into two groups. existence subfamilies (Lithospermeae Boragineae) Boraginaceae is strongly supported. Our study provides valuable on

Language: Английский

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Chloroplast Genome Draft of Dryobalanops aromatica Generated Using Oxford Nanopore Technology and Its Potential Application for Phylogenetic Study

Forests, Journal Year: 2021, Volume and Issue: 12(11), P. 1515 - 1515

Published: Nov. 3, 2021

Kapur (Dryobalanops aromatica) is an important dipterocarp species currently classified as vulnerable by the IUCN Red List Threatened Species. Science-based conservation and restoration efforts are needed, which can be supported new genomic data generated from technologies, including MinION Oxford Nanopore Technology (ONT). ONT allows affordable long-read DNA sequencing, but this technology still rarely applied to native Indonesian forest trees. Therefore, study aimed generate whole genome datasets through use part of these construct draft chloroplast analyze universal barcode-based genetic relationships for D. aromatica. The method included isolation, library preparation, bioinformatics analysis, phylogenetic tree construction. Results showed that sequencing aromatica resulted in 1.55 Gb sequences a partial (148,856 bp) was successfully constructed. relationship analyzed using two selected barcodes (rbcL matK), its combination genus Dryobalanops had close indicated adjacent branches between species. matK rbcL genes closely related rappa, whereas gene group separation rappa. recommended future or phylogenomic analysis

Language: Английский

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