Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species
Abstract 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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2017-09-01
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| Series: | Botanical Studies |
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| Online Access: | http://link.springer.com/article/10.1186/s40529-017-0192-8 |
| _version_ | 1818304822211772416 |
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| author | Yingang Li Wuqin Xu Wentao Zou Dongyue Jiang Xinhong Liu |
| author_facet | Yingang Li Wuqin Xu Wentao Zou Dongyue Jiang Xinhong Liu |
| author_sort | Yingang Li |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-13T06:16:48Z |
| format | Article |
| id | doaj.art-39f7e9357d0d4fa0b426ae78ec7481e0 |
| institution | Directory Open Access Journal |
| issn | 1999-3110 |
| language | English |
| last_indexed | 2024-12-13T06:16:48Z |
| publishDate | 2017-09-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Botanical Studies |
| spelling | doaj.art-39f7e9357d0d4fa0b426ae78ec7481e02022-12-21T23:56:57ZengSpringerOpenBotanical Studies1999-31102017-09-0158111010.1186/s40529-017-0192-8Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) speciesYingang Li0Wuqin Xu1Wentao Zou2Dongyue Jiang3Xinhong Liu4Zhejiang Academy of ForestryKey Laboratory of Conservation Biology for Endangered Wildlife of Ministry of Education, College of Life Sciences, Zhejiang UniversityInstitute of Tropical Forestry, Chinese Academy of ForestryZhejiang Academy of ForestryZhejiang Academy of ForestryAbstract 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.http://link.springer.com/article/10.1186/s40529-017-0192-8Phoebe chekiangensisPhoebe bourneiChloroplast genomesRepeat analysisSSRsDivergent regions |
| spellingShingle | Yingang Li Wuqin Xu Wentao Zou Dongyue Jiang Xinhong Liu Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species Botanical Studies Phoebe chekiangensis Phoebe bournei Chloroplast genomes Repeat analysis SSRs Divergent regions |
| title | Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species |
| title_full | Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species |
| title_fullStr | Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species |
| title_full_unstemmed | Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species |
| title_short | Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species |
| title_sort | complete chloroplast genome sequences of two endangered phoebe lauraceae species |
| topic | Phoebe chekiangensis Phoebe bournei Chloroplast genomes Repeat analysis SSRs Divergent regions |
| url | http://link.springer.com/article/10.1186/s40529-017-0192-8 |
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