The complete chloroplast genome sequence of <i>Trigonotis peduncularis</i> (Boraginaceae)

Wu, Jianguo; Li, Huimin; Lei, Jin-man; Liang, Ze-rui

doi:10.1080/23802359.2022.2048212

Cited by 8 publications

(5 citation statements)

References 8 publications

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“…The analysis demonstrated that the M. sikkimensis chloroplast genome spanned a length of 149,428 bp, and it featured the circular quadripartite typical of chloroplast genomes, consisting of the LSC, SSC, and a pair of IR regions. Gene annotation indicated that the genome contains 112 genes, which include 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, which is consistent with the genomic structure and gene quantity observed in the chloroplasts of other species within the Boraginaceae family [47][48][49][50][51]. Introns were crucial for the regulatory mechanisms that control gene expression.…”

Section: Discussionsupporting

confidence: 68%

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Gao,

Chen,

et al. 2024

Genes

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The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species.

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Section: Discussionsupporting

confidence: 68%

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Gao,

Chen,

et al. 2024

Genes

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“…The C. monoica cp genome typically exists as a double-stranded circular molecule with two inverted repeats (IR) and one large single copy (LSC) [38,39]. Our assembly and annotation results show that the C. monoica cp genome length is 148,711 bp, which is in the range of other Boraginaceae species [40,41], displaying similar genome structures and gene arrangements. While the tRNA and rRNA gene compositions of the three Boraginaceae species are similar, some differences are observed in the number of PCGs.…”

Section: Discussionmentioning

confidence: 79%

The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis

Alshegaihi

Mansour

Alrobaish

et al. 2023

Genes

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Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897–26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).

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“…In this research, we presented the plastomes of two taxa belonging to the Cordiaceae. The plastomes of C. monoica and C. sinensis structurally resembled the plastomes of other Boraginales species [54,55]. The plastome sizes of C. monoica and C. sinensis ranged from 151,813 bp to 152,050 bp, respectively (Figure 1).…”

Section: Discussionmentioning

confidence: 87%

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

Alawfi,

Albokhari

2023

Forests

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Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia sinensis were sequenced, and their cp genomes were then characterized, analyzed, and compared to those of closely related taxa. The lengths of the cp genomes of C. monoica and C. sinensis were 151,813 bp and 152,050 bp, respectively. Both genomes consisted of 114 genes, divided into 4 ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. We observed a unique gene inversion in the trnM-rbcL region of both Cordia species. The long repeats analysis revealed that both species’ chloroplast genomes contained forward and palindromic repeats. The simple sequence repeats (SSRs) analysis detected 155 microsatellites in each genome, with the majority being mononucleotide repeats (A/T). Phylogenetic analysis based on maximum likelihood and Bayesian analyses confirmed two major clades in the order Boraginales: clade I comprised Boraginaceae, while clade II included Cordiaceae, Ehretiaceae, and Heliotropiaceae. This study expands our knowledge of the evolutionary relationships across the order Boraginales and offers useful genetic resources.

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The complete chloroplast genome sequence of Trigonotis peduncularis (Boraginaceae)

Cited by 8 publications

References 8 publications

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

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