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The complete chloroplast genome sequence of Dalbergia oliveri.

ABSTRACT: The first complete chloroplast genome (cpDNA) sequence of Dalbergia oliveri was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 156,750 bp in length, contains a large single copy region (LSC) of 156,750 bp and a small single copy region (SSC) of 19,510 bp, which were separated by a pair of inverted repeats (IR) regions of 25,687 bp. The genome contains 127 genes, including 82 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.9%, and the corresponding values of the LSC, SSC, and IR regions are 33.4%, 28.8%, and 42.8%, respectively. Further phylogenomic analysis showed that D. oliveri and other species of Dalbergia genus clustered in a unique clade in Dalbergieae with Fabaceae family.

SUBMITTER: Zhang J

PROVIDER: S-EPMC7748691 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications.

Project description:The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

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Characterization of the complete chloroplast genome of Dalbergia cultrata (Leguminosae).

Project description:Dalbergia cultrata is a Near Threatened species with high ecological and economic values. In this study, its chloroplast genome was assembled using Illumina pair-end sequencing dataset. The chloroplast genome has a quadripartite structure with 156,385?bp in length and contains a pair of 16,392?bp inverted repeat (IR) regions, which were separated by large single copy (LSC: 86,040?bp) region and small single copy (SSC: 37,561?bp) region. A total of 121 genes were annotated, including 77 protein-coding genes (PCGs), 36 tRNAs, and 8 rRNAs. The overall GC content was 36.1%. The phylogenetic analysis revealed that D. cultrata has close relationship to D. hainanensis and D. odorifera. This complete chloroplast genome can be readily used for population genetic studies of D. cultrata.

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The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

Project description:We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

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Complete chloroplast genome sequence of Amomum villosum.

Project description:The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.

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Project description:The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.

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