{"title":"稀有物种 Libellula melli 线粒体基因组的特征和系统发育意义","authors":"Binquan Lin, Hao Chen, Jiayu Li, Jian Liao","doi":"10.1016/j.genrep.2024.101986","DOIUrl":null,"url":null,"abstract":"<div><p>This study sequenced and assembled the mitochondrial genome of the rare dragonfly species <em>Libellula melli</em>, and submitted the results to the NCBI GenBank database, obtaining the accession number PP588458. The mitochondrial genome spans a total length of 15,149 bp, encompassing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region or D-loop. Of these, 25 genes and segments are located on the heavy strand (H-strand), while the remaining 13 reside on the light strand (L-strand). The nucleotide composition of the <em>L. melli</em> mitochondrial genome exhibits a prominent AT bias (AT = 73.3 %), with T, C, A, and G bases comprising 34.5 %, 15.6 %, 38.8 %, and 11.1 % respectively, displaying a positive AT skew of 0.059. Among the 13 PCGs, the primary start codons are ATT, ATG, and TTG, while the primary stop codons are TAA, with instances of TA(C) and T(AT) also observed. RSCU analysis reveals that the most frequently used codon is UUA, with an RSCU value of 3.75, encoding leucine (Leu). The secondary structures of the proteins encoded by the 13 PCGs generally exhibit a trend of α-helix > random coil > extended strand > β-turn. Phylogenetic analysis uncovers the phylogenetic relationships of <em>L</em>. <em>melli</em> within the reported Libellulidae species, revealing (((((((<em>L. melli</em> + <em>L. quadrimaculata</em>) + <em>L. angelina</em>) + ((<em>O. chrysis</em> + <em>O. glaucum</em>) + <em>O. albistylum</em>)) + ((<em>C. servilia servilia</em> + <em>T. virginia</em>) + <em>N. fulvia</em>) + (<em>L. albifrons</em> + <em>S. eroticum</em>)) + (<em>P. flavescens</em> + <em>T. aurora</em>)) + (<em>D. phaon</em> + <em>H. croceus</em>)) + (<em>B. contaminate</em> + <em>P. zonata</em>)). This study provides insights into the mitochondrial genome and its characteristics of this rare dragonfly species, contributing to our understanding of the intricate evolutionary relationships within the Odonata order. The data obtained serve as a foundation for further exploration of the complex phylogenetic relationships among dragonfly insects.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Characteristics and phylogenetic implications of the mitochondrial genome of a rare species, Libellula melli\",\"authors\":\"Binquan Lin, Hao Chen, Jiayu Li, Jian Liao\",\"doi\":\"10.1016/j.genrep.2024.101986\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>This study sequenced and assembled the mitochondrial genome of the rare dragonfly species <em>Libellula melli</em>, and submitted the results to the NCBI GenBank database, obtaining the accession number PP588458. The mitochondrial genome spans a total length of 15,149 bp, encompassing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region or D-loop. Of these, 25 genes and segments are located on the heavy strand (H-strand), while the remaining 13 reside on the light strand (L-strand). The nucleotide composition of the <em>L. melli</em> mitochondrial genome exhibits a prominent AT bias (AT = 73.3 %), with T, C, A, and G bases comprising 34.5 %, 15.6 %, 38.8 %, and 11.1 % respectively, displaying a positive AT skew of 0.059. Among the 13 PCGs, the primary start codons are ATT, ATG, and TTG, while the primary stop codons are TAA, with instances of TA(C) and T(AT) also observed. RSCU analysis reveals that the most frequently used codon is UUA, with an RSCU value of 3.75, encoding leucine (Leu). The secondary structures of the proteins encoded by the 13 PCGs generally exhibit a trend of α-helix > random coil > extended strand > β-turn. Phylogenetic analysis uncovers the phylogenetic relationships of <em>L</em>. <em>melli</em> within the reported Libellulidae species, revealing (((((((<em>L. melli</em> + <em>L. quadrimaculata</em>) + <em>L. angelina</em>) + ((<em>O. chrysis</em> + <em>O. glaucum</em>) + <em>O. albistylum</em>)) + ((<em>C. servilia servilia</em> + <em>T. virginia</em>) + <em>N. fulvia</em>) + (<em>L. albifrons</em> + <em>S. eroticum</em>)) + (<em>P. flavescens</em> + <em>T. aurora</em>)) + (<em>D. phaon</em> + <em>H. croceus</em>)) + (<em>B. contaminate</em> + <em>P. zonata</em>)). This study provides insights into the mitochondrial genome and its characteristics of this rare dragonfly species, contributing to our understanding of the intricate evolutionary relationships within the Odonata order. The data obtained serve as a foundation for further exploration of the complex phylogenetic relationships among dragonfly insects.</p></div>\",\"PeriodicalId\":12673,\"journal\":{\"name\":\"Gene Reports\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.0000,\"publicationDate\":\"2024-07-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Gene Reports\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2452014424001092\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2452014424001092","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
摘要
本研究对珍稀蜻蜓物种Libellula melli的线粒体基因组进行了测序和组装,并将结果提交至NCBI GenBank数据库,获得了登录号PP588458。线粒体基因组总长度为 15,149 bp,包括 13 个蛋白质编码基因(PCGs)、22 个 tRNA 基因、2 个 rRNA 基因和一个控制区或 D 环。其中,25 个基因和片段位于重链(H 链)上,其余 13 个基因和片段位于轻链(L 链)上。L. melli 线粒体基因组的核苷酸组成显示出明显的 AT 偏倚(AT = 73.3 %),T、C、A 和 G 碱基分别占 34.5 %、15.6 %、38.8 % 和 11.1 %,显示出 0.059 的正 AT 偏移。在 13 个 PCGs 中,主要的起始密码子是 ATT、ATG 和 TTG,而主要的终止密码子是 TAA,此外还发现有 TA(C) 和 T(AT) 的情况。RSCU 分析显示,最常用的密码子是 UUA,RSCU 值为 3.75,编码亮氨酸(Leu)。13 个 PCGs 所编码蛋白质的二级结构总体上呈现出α-螺旋> 随机线圈> 扩展链> β-转折的趋势。系统发育分析揭示了 L. melli 在已报道的 Libellulidae 物种中的系统发育关系,发现 (((((((L. melli + L. quadrimaculata) + L. angelina) + ((O. chrysis + O. gla.Chrysis + O. glaucum) + O. albistylum)) + ((C. servilia servilia + T. virginia) + N. fulvia) + (L. albifrons + S. eroticum)) + (P. flavescens + T. aurora)) + (D. phaon + H. croceus))+ B. contaminate + P. zonata))。这项研究深入揭示了这一罕见蜻蜓物种的线粒体基因组及其特征,有助于我们了解蜻蜓目内部错综复杂的进化关系。获得的数据为进一步探索蜻蜓昆虫之间复杂的系统发育关系奠定了基础。
Characteristics and phylogenetic implications of the mitochondrial genome of a rare species, Libellula melli
This study sequenced and assembled the mitochondrial genome of the rare dragonfly species Libellula melli, and submitted the results to the NCBI GenBank database, obtaining the accession number PP588458. The mitochondrial genome spans a total length of 15,149 bp, encompassing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region or D-loop. Of these, 25 genes and segments are located on the heavy strand (H-strand), while the remaining 13 reside on the light strand (L-strand). The nucleotide composition of the L. melli mitochondrial genome exhibits a prominent AT bias (AT = 73.3 %), with T, C, A, and G bases comprising 34.5 %, 15.6 %, 38.8 %, and 11.1 % respectively, displaying a positive AT skew of 0.059. Among the 13 PCGs, the primary start codons are ATT, ATG, and TTG, while the primary stop codons are TAA, with instances of TA(C) and T(AT) also observed. RSCU analysis reveals that the most frequently used codon is UUA, with an RSCU value of 3.75, encoding leucine (Leu). The secondary structures of the proteins encoded by the 13 PCGs generally exhibit a trend of α-helix > random coil > extended strand > β-turn. Phylogenetic analysis uncovers the phylogenetic relationships of L. melli within the reported Libellulidae species, revealing (((((((L. melli + L. quadrimaculata) + L. angelina) + ((O. chrysis + O. glaucum) + O. albistylum)) + ((C. servilia servilia + T. virginia) + N. fulvia) + (L. albifrons + S. eroticum)) + (P. flavescens + T. aurora)) + (D. phaon + H. croceus)) + (B. contaminate + P. zonata)). This study provides insights into the mitochondrial genome and its characteristics of this rare dragonfly species, contributing to our understanding of the intricate evolutionary relationships within the Odonata order. The data obtained serve as a foundation for further exploration of the complex phylogenetic relationships among dragonfly insects.
Gene ReportsBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.30
自引率
7.70%
发文量
246
审稿时长
49 days
期刊介绍:
Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.