Tianze Wu, Gang Deng, Qinggang Yin, Shilin Chen, Yongping Zhang, Bo Wang, Li Xiang, Xia Liu
{"title":"林柏属植物叶绿体全基因组序列的鉴定与分子进化分析。","authors":"Tianze Wu, Gang Deng, Qinggang Yin, Shilin Chen, Yongping Zhang, Bo Wang, Li Xiang, Xia Liu","doi":"10.1139/gen-2022-0050","DOIUrl":null,"url":null,"abstract":"<p><p><i>Periploca forrestii</i>, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of <i>P. forrestii</i> based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on <i>P. forrestii</i>. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the <i>psaI</i> and <i>ycf2</i> genes, which might reflect specific adaptions to the <i>P. forrestii</i> particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important <i>P. forrestii</i> genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 2","pages":"34-50"},"PeriodicalIF":2.3000,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Characterization and molecular evolution analysis of <i>Periploca forrestii</i> inferred from its complete chloroplast genome sequence.\",\"authors\":\"Tianze Wu, Gang Deng, Qinggang Yin, Shilin Chen, Yongping Zhang, Bo Wang, Li Xiang, Xia Liu\",\"doi\":\"10.1139/gen-2022-0050\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><i>Periploca forrestii</i>, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of <i>P. forrestii</i> based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on <i>P. forrestii</i>. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the <i>psaI</i> and <i>ycf2</i> genes, which might reflect specific adaptions to the <i>P. forrestii</i> particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important <i>P. forrestii</i> genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.</p>\",\"PeriodicalId\":12809,\"journal\":{\"name\":\"Genome\",\"volume\":\"66 2\",\"pages\":\"34-50\"},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2023-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1139/gen-2022-0050\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1139/gen-2022-0050","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence.
Periploca forrestii, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of P. forrestii based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on P. forrestii. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the psaI and ycf2 genes, which might reflect specific adaptions to the P. forrestii particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important P. forrestii genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.
期刊介绍:
Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.