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Characterization of the complete chloroplast genome of a Chinese Endangered species Cymbidium mastersii.

ABSTRACT: Cymbidium mastersii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies for C. mastersii of chloroplast genome sequencing. The genome features of C. mastersii and the phylogenetic relationships were reported and established. The complete chloroplast genome is 156,317 bp in length, consisting of a pair of inverse duplication regions 26,544 bp, a large single-copy region 85,360 bp and a small single-copy region 17,869 bp. The entire genome contains 73 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mastersii is more closely related to Cymbidium eburneum.

SUBMITTER: Ling Q

PROVIDER: S-EPMC7971198 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome of a Chinese endangered species Cymbidium mannii.

Project description:Cymbidium mannii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. mannii. The genome features of C. mannii and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 152,544 bp in length, consisting of a pair of inverse duplication regions 25,357 bp, a large single-copy region 86,014 bp and a small single-copy region 15,816 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mannii is more closely related to Cymbidium aloifolium.

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MITOGENOME ANNOUNCEMENTSCharacterization of the complete chloroplast genome of the Chinese endangered species Cymbidium iridioides D. Don.

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The complete chloroplast genome of Cymbidium serratum (Orchidaceae): a rare and Endangered species endemic to Southwest China.

Project description:Cymbidium serratum is a dominant species in the large orchid family with beautiful flowers, thick petals, and long flowering periods, and has a long history of cultivation in Southwest China. However, its wild resources have been threatened with extinction due to environmental degradation and artificial exploitation. In this study, the complete chloroplast genome of C. serratum was obtained through Illumina sequencing. The size of chloroplast genome of C. serratum is 149,998 bp, including large single-copy (LSC) and small single-copy (SSC) regions over 84,854 bp and 13,926 bp, respectively, and two inverted repeats (IRs) of 25,609 bp. The total GC content was 37.11%. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The maximum-likelihood phylogenetic tree indicated that C. serratum is a sister species with the clade composed of C. faberi and C. goeringii. The complete chloroplast genome of C. serratum will contribute to protecting this highly endangered species, and provide genetic information about genetic diversity and sustainable use.

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Complete chloroplast genome of an orchid species Cymbidium floribundum Lindl.

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| S-EPMC7706694 | biostudies-literature

Characterization of the complete chloroplast genome of a hybrid species Cymbidium tracyanum var 'huanghua' × Cymbidium faberi cv 'huanghui'.

Project description:Cymbidium tracyanumvar 'huanghua' × Cymbidium fabericv 'huanghui' is a hybrid species with important ornamental value. In the research, Illumina high-throughput sequencing technologies was used to sequence the chloroplastic genome of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui'. The genome features of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' and the phylogenetic relationships were reported and established. The total length of the complete chloroplast genome is 154,741 bp, consisting of a pair of inverse duplication regions 26,968 bp, a large single-copy region 84,410 bp and a small single-copy region 16,395 bp. The complete genome contains 73 protein-coding genes (PCGs), The entire genome contains 73 genes that encode proteins, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree revealed that Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' is more closely related to Cymbidium erythraeum.

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

Project description:BACKGROUND:Phoebe (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. RESULTS:We 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. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

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