Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: Jan. 18, 2017

Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They positioned phylogenetically large subclade rosids (in eudicots) which contain more than 25% all angiosperms. commonly bloom summer till fall and significant value in city landscape environmental protection. Morphological traits shared inter-specifically among plants certain extent also influenced by conditions different developmental stages. Thus, classification at species cultivar levels is still challenging task. Chloroplast (cp) genome sequences have been proven be an informative valuable source cp DNA markers for genetic diversity evaluation. In this study, complete genomes three were newly sequenced, other published retrieved comparative analyses order obtain upgraded understanding application information genomes. The six ranged 152,049 bp (L. subcostata) 152,526 speciosa) length. We analyzed nucleotide substitutions, insertions/deletions, simple sequence repeats genomes, discovered 12 relatively highly variable regions that will potentially provide plastid further taxonomic, phylogenetic, population genetics studies Lagerstroemia. phylogenetic relationships taxa inferred datasets obtained high support, indicating data may useful resolving genus.

Language: Английский

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Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: July 20, 2019

Prunus mume Sieb. et Zucc., P. armeniaca L., and salicina L. are economically important fruit trees in temperate regions. These species taxonomically perplexing because of shared interspecific morphological traits variation, which mainly attributed to hybridization. The chloroplast is cytoplasmically inherited often used for evolutionary studies. We sequenced the complete genomes mume, armeniaca, using Illumina sequencing followed by de novo assembly. three exhibit a typical quadripartite structure with conserved genome arrangement, structure, moderate divergence. lengths 157,815, 157,797, 157,916 bp, respectively. length large single-copy region (LSC) 86,113, 86,283, 86,122 SSC 18,916, 18,734, 19,028 bp; IR 26,393, 26,390, 26,383 Each encodes 133 genes, including 94 protein-coding, 31 tRNA, eight rRNA genes. Differential gene analysis revealed that trnY-ATA unique armeniaca; contrast, trnI-TAT only present salicina, though position these differs. Further comparative sequences ORF genes linked regions rps16 atpA, atpH atpI, trnc-GCA psbD, ycf3 atpB, rpL32 ndhD significantly different may be as molecular markers taxonomic Phylogenetic evolution suggests has closer genetic relationship than salicina.

Language: Английский

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Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 7

Published: Jan. 5, 2017

Juglans L. (walnuts and butternuts) is an economically ecologically important genus in the family Juglandaceae. All are nut timber trees. regia (Common walnut), J. sigillata (Iron cathayensis (Chinese hopeiensis (Ma mandshurica (Manchurian walnut) native to or naturalized China. A strongly supported phylogeny of these five species not available due a lack informative molecular markers. We compared complete chloroplast genomes determined phylogenetic relationships among Chinese using IIumina sequencing. The plastid ranged from 159,714 160,367 bp encoding 128 functional genes, including 88 protein-coding genes 40 tRNA each. map variability across was produced that included single nucleotide variants, indels (insertions deletions), large structural as well differences simple sequence repeats (SSR) repeat sequences. Molecular division walnut into two previously recognized sections (Juglans/Dioscaryon Cardiocaryon) with 100 % bootstrap (BS) value cp genomes, protein coding sequences (CDS), introns spacers (IGS) data. availability will provide genetic information for identifying hybrids, taxonomy, phylogeny, evolution Juglans, also insight utilization plants.

Language: Английский

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Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae

Genomics, Journal Year: 2019, Volume and Issue: 112(2), P. 1454 - 1463

Published: Aug. 23, 2019

Language: Английский

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Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: Oct. 6, 2017

The Chenopodium genus comprises approximately 150 species, including C. quinoa and album, two important crops with high nutritional value. To elucidate the phylogenetic relationship between complete chloroplast (cp) genomes of these species were obtained by next generation sequencing. We performed comparative analysis sequences and, using InDel markers, inferred phylogeny genetic diversity genus. cp genome is 152,167 bp (C. quinoa) 152,099 album) long. In total, 119 genes (78 protein-coding, 37 tRNA, 4 rRNA) identified. found 14 15 tandem repeats (TRs); TRs present in both album each had one species-specific TR. trnI-GAU intron contained or copies (66 bp); marker was designed based on copy number variation TRs. Using we detected this TR four hybridum, pumilio, ficifolium, koraiense, but not glaucum. A comparison coding non-coding regions revealed divergent sites. Nucleotide greater than 0.025 17 regions—14 located large single region, inverted repeats, small region. 59 protein-coding from 25 taxa resolved Chenopodioideae monophyletic sister to Betoideae. plastid molecular markers divergence hotspot will help resolve relationships Chenopodium.

Language: Английский

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The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: March 10, 2017

The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, yellow passion fruit (Passiflora edulis) is considerable economic importance, both for juice production and consumption as fresh fruit. availability chloroplast genomes (cp genomes) their sequence comparisons has led a better understanding evolutionary relationships within plant taxa. this study, we obtained complete nucleotide Passiflora edulis genome, first entirely sequenced family. We determined structure organization, also performed phylogenomic studies on order Malpighiales Fabids clade. P. genome characterized by presence two copies an inverted repeat (IRA IRB) 26,154 bp, each separating small single-copy (SSC) region 13,378 bp large (LSC) 85,720 bp. annotation resulted identification 105 unique genes, including 30 tRNAs, 4 rRNAs 71 protein coding genes. Also, 36 repetitive elements 85 SSRs (microsatellites) were identified. cp differs from that other because rearrangement events detected means comparison based 22 Malpighiales. rearrangements three inversions 46,151 3,765 1,631 located LSC region. Phylogenomic analysis strongly supported trees, but could be consequence limited taxonomic sampling used. Our results have provided Fabids, confirming potential sequences inferring utility long reads generating very accurate biological information.

Language: Английский

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Molecular evolution of chloroplast genomes in Monsteroideae (Araceae)

Planta, Journal Year: 2020, Volume and Issue: 251(3)

Published: Feb. 28, 2020

Language: Английский

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Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution

International Journal of Molecular Sciences, Journal Year: 2018, Volume and Issue: 19(7), P. 1847 - 1847

Published: June 22, 2018

Urophysa is a Chinese endemic genus comprising two species, rockii and henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these species their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate intra- interspecies variations, infer phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure detected, genome size from 158,473 158,512 bp, consisting pair inverted repeats separated by small single-copy region large region. We analyzed nucleotide diversity repeated sequences components conducted positive selection analysis codon-based substitution on coding sequence (CDS). Seven regions were found possess relatively high diversity, numerous variable simple (SSR) markers detected. Six genes (atpA, rpl20, psaA, atpB, ndhI, rbcL) resulted have posterior probabilities codon sites in analysis, which means that six may be under great pressure. The visualization results showed amino acid properties across each column all are different genera. All abundant repeats, will provide potential plastid for further taxonomic, phylogenetic, population genetics studies its relatives. Phylogenetic analyses based 79 genes, whole CDS same topologies support, U. closely clustered henryi within genus, S. adoxoides as closest relative. Therefore, cp interesting insights valuable information can identify related reconstruct phylogeny.

Language: Английский

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Comparative analyses of chloroplast genomes among three Firmiana species: Identification of mutational hotspots and phylogenetic relationship with other species of Malvaceae

Plant Gene, Journal Year: 2019, Volume and Issue: 19, P. 100199 - 100199

Published: July 10, 2019

Language: Английский

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Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Aug. 22, 2019

Abstract The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most these species are found in temperate climates Northern Hemisphere. Furthermore, as a large number new continue to be identified, phylogenetic classification based on morphological characteristics few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present use complete chloroplast genome sequences genome-scale studies . We sequenced assembled four genomes retrieved five published from GenBank. All nine were used for genomic comparison inference. genomes, ranging 152,387 bp 154,482 length, exhibited conservation structure, gene organization order. Subsequently, observed expansion IRs basal monocot Acorus americanus , identified 814 simple sequence repeats, 131 tandem 154 dispersed repeats 109 palindromic six highly variable regions. relationships inferred obtained high support, indicating that data useful further resolution phylogeny

Language: Английский

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