A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomi...A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental pressures.Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.展开更多
生长阻滞和DNA损伤诱生蛋白45 （growth arrest and DNA damage inducible protein 45,Gadd45）基因在胚胎发育和性别决定中起重要作用.本研究通过RACE方法在半滑舌鳎（Cynoglossus semilaevis）中克隆得到了1个Gadd45g同源基因,命名为G...生长阻滞和DNA损伤诱生蛋白45 （growth arrest and DNA damage inducible protein 45,Gadd45）基因在胚胎发育和性别决定中起重要作用.本研究通过RACE方法在半滑舌鳎（Cynoglossus semilaevis）中克隆得到了1个Gadd45g同源基因,命名为Gadd45g3.该基因全长1 147 bp,编码155个氨基酸残基.氨基酸序列分析表明,半滑舌鳎Gadd45g3与其他鱼类Gadd45g-like的同源性为79％～88％,与硬骨鱼和高等脊椎动物的Gadd45g同源性为58％～67％.对多个物种的Gadd45g同源基因的CDS区进行Ka/Ks分析,发现Ka/Ks均小于0.3.FISH结果显示,半滑舌鳎Gadd45g3基因位于常染色体上.实时荧光定量PCR结果显示,Gadd45g3在雌雄成鱼的脑中都有很高的表达,说明其参与了神经发育;在成熟性腺中,Gadd45g3的表达具有精巢特异性,说明Gadd45g3是性别相关基因;而在不同发育时期的性腺中,Gadd45g3的表达量在孵化后20 d的雄性仔鱼中显著高于同龄雌鱼（P＜0.05）,但在孵化后95 d的雌雄仔鱼中均有高表达,说明在半滑舌鳎性别决定和性腺发育中起着重要作用.展开更多
We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we ...We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.展开更多
基金supported by the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2022QNLM030004)Hainan Science and Technology Department(ZDKJ2019011)+2 种基金Open Project Fund of Key Laboratory of Sustainable Development of Polar Fisheries,Ministry of Agriculture and Rural Affairs of PRC(2022OPF02)State Key R&D Project(2021YFF0502500)Qingdao Postdoctoral Applied Research Project(JZ2223j06100)。
文摘A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral species.Assessments of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial sequences.The nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental pressures.Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species formation.This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.
文摘生长阻滞和DNA损伤诱生蛋白45 （growth arrest and DNA damage inducible protein 45,Gadd45）基因在胚胎发育和性别决定中起重要作用.本研究通过RACE方法在半滑舌鳎（Cynoglossus semilaevis）中克隆得到了1个Gadd45g同源基因,命名为Gadd45g3.该基因全长1 147 bp,编码155个氨基酸残基.氨基酸序列分析表明,半滑舌鳎Gadd45g3与其他鱼类Gadd45g-like的同源性为79％～88％,与硬骨鱼和高等脊椎动物的Gadd45g同源性为58％～67％.对多个物种的Gadd45g同源基因的CDS区进行Ka/Ks分析,发现Ka/Ks均小于0.3.FISH结果显示,半滑舌鳎Gadd45g3基因位于常染色体上.实时荧光定量PCR结果显示,Gadd45g3在雌雄成鱼的脑中都有很高的表达,说明其参与了神经发育;在成熟性腺中,Gadd45g3的表达具有精巢特异性,说明Gadd45g3是性别相关基因;而在不同发育时期的性腺中,Gadd45g3的表达量在孵化后20 d的雄性仔鱼中显著高于同龄雌鱼（P＜0.05）,但在孵化后95 d的雌雄仔鱼中均有高表达,说明在半滑舌鳎性别决定和性腺发育中起着重要作用.
基金funded by the National Basic Research Program of China (973 Program) to JY (Grant No.2006CB910404)
文摘We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.
