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The complete chloroplast genome of Pterospermum menglunense (Sterculiaceae), an endangered species.

ABSTRACT: Pterospermum menglunense is the endangered plant species of the genus Pterospermum in the family Sterculiaceae. In the study, the complete genome was 162,421bp in length, including of two inverted repeats (IRA and IRB, 25,572 bp), separated by a large single-copy region (LSC, 90,754 bp) and a small single-copy region (SSC, 20,523 bp). The genome annotation reveals a total of 132 genes, including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 87 protein-coding (PCG) genes. The phylogenetic tree showed P. menglunense is closely related to Pterospermum kingtungense.

SUBMITTER: Guan-Song Y

PROVIDER: S-EPMC8008881 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Pterospermum kingtungense, a Critically Endangered species.

Project description:Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.

| S-EPMC7801019 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BackgroundPhoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus.ResultsWe sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies.ConclusionThis study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

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The complete chloroplast genome sequence of Melochia corchorifolia Linnaeus, 1753 (Sterculiaceae).

Project description:Melochia corchorifolia Linnaeus, 1753, is a weedy tropical plant of the Sterculiaceae family and has medicinal value. We sequenced the complete chloroplast genome of M. corchorifolia using Illumina high-throughput sequencing and examined phylogenetic relationships with closely related species. The assembled chloroplast genome of M. corchorifolia was 163,693 bp long and contained a pair of inverted repeats of 29,729 bp, separated by a large single-copy sequence of 84,350 bp and a small single-copy region of 19,885 bp. A total of 136 genes were annotated across the entire chloroplast genome, including 37 transfer RNA, 8 ribosomal RNA, and 91 protein-coding genes. The GC content of the complete cp genome was 37.27%. The phylogenetic tree indicated that M. corchorifolia is closely related to Melochia pyramidata (Malvaceae). These results would provide useful information for future phylogenetic, taxonomic, and evolutionary studies on Sterculiaceae and Malvaceae.

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The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae).

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The complete chloroplast genome of the endangered species Cephalotaxus hainanensis (Cephalotaxaceae).

Project description:Cephalotaxus hainanensis is an endangered tree endemic to China with high medicinal values. In this study, the complete chloroplast genome of C. hainanensis was de novo assembled using Illumina high-throughput sequencing technology. The whole chloroplast genome was 136,877?bp long with an asymmetric base composition (32.6% A, 17.6% C, 17.4% G and 32.4% T). The genome annotation predicted a total of 114 genes, including 82 protein-coding genes, 28 tRNA genes, and four rRNA genes. The neighbour-joining phylogenetic analysis based on 41 complete chloroplast genome sequences showed that C. hainanensis was more closely related to the congeneric C. sinensis. The assembled chloroplast genome of C. hainanensis will provide useful genomic data both for the phylogenetic research of Cephalotaxus and the conservation of this endangered species.

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The complete chloroplast genome of an Endangered species Cymbidium Nanulum (Orchidaceae).

Project description:Cymbidium nanulum Y.S.Wu & S.C.Chen is an IUCN Red listed Endangered species and distributes in South-Central China and Hainan. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. nanulum. The complete chloroplast (cp) genome sequence of C. nanulum was 149,776 bp in length. It presented a typical quadripartite structure including one large single-copy region (LSC, 85,392 bp), one small single-copy region (SSC, 14,210 bp), and two inverted repeat regions (IRs, 25,087 bp). The cp genome encoded 133 genes, of which 104 were unique genes (77 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. nanulum was closely related to other species of genus Cymbidium.

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The complete chloroplast genome of Cycas Szechuanensis, an extremely endangered species.

Project description:In this study, we determined the complete chloroplast genome of Cycas szechuanensis (Cycadaceae, Cycas) using the Illumina sequencing data. The genome is 162,083 bp in length, including a pair of inverted repeats (IRs) of 25,003 bp each, which are separated by a large single-copy region (LSC) and a small single-copy region (SSC) with the size of 88,970 and 23,108 bp, respectively. The genome comprises 131 encoded genes in total, including 86 protein-coding genes (82 PCG species), 8 ribosomal RNA genes (4 rRNA species), and 37 transfer RNA genes (30 tRNA species). The overall GC content of the C. szechuanensis chloroplast genome is 39.42%, while the LSC, SSC, and IRs occupy 38.70, 42.03 and 36.52%, respectively. Based on complete chloroplast genome sequences from 13 species, we reconstructed the phylogenetic relationship of the 13 species and found that C. szechuanensis is closely related to C. debaoensis.

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The complete chloroplast genome of an endangered species Apostasia ramifera (Orchidaceae).

Project description:Apostasia ramifera S. C. Chen & K. Y. Lang 1986 is a Chinese endemic and endangered orchid. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of A. ramifera. The cp genome was 157,518 bp in length with a typical quadripartite structure, which was comprised of one large single-copy region (LSC, 86,353 bp) and one small single-copy region (SSC, 16,445 bp) separated by two inverted repeat regions (IRs, 27,360 bp). The cp genome encoded 133 genes, which included 87 protein-coding genes, 38 tRNAs and eight rRNAs. The average GC content of the genome is 35.8%. The phylogenetic analysis showed that A. ramifera was sister with A. wallichii and then nested in the other Apostasia species.

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Complete chloroplast genome sequence of Heritiera angustata (Malvaceae): an endangered plant species.

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