Characterization of mitochondrial genome of sea cucumber Stichopus horrens:A novel gene arrangement in Holothuroidea

The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens （Holothuroidea： Sdchopodidae： Stichopus） is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene （had6） and five tRNA genes （tRNAser（UcN）, tRNAGtn, tRNAAla, tRNA val, tRNAASp） which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases （AT skew=0.025; GC skew=-0.188）. A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes ex- cept nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu （16.29%）, Ser （10.34%） and Phe （8.37%）. All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.

Analysis of environmental selection pressure of superoxide dismutase in deep-sea sea cucumber

Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is essential for the survival of sea cucumbers.Six MnSODs were identified from the transcriptomes of deep and shallow-sea sea cucumbers.To explore their environmental adaptation mechanism,we conducted environmental selection pressure analysis through the branching site model of PAML software.We obtained night positive selection sites,and two of them were significant(97F→H,134K→V):97F→H located in a highly conservative characteristic sequence,and its polarity c hange might have a great impact on the function of MnSOD;134K→V had a change in piezophilic a bility,which might help MnSOD adapt to the environment of high hydrostatic pressure in the deepsea.To further study the effect of these two positive selection sites on MnSOD,we predicted the point mutations of F97H and K134V on shallow-sea sea cucumber by using MAESTROweb and PyMOL.Results show that 97F→H,134K→V might improve MnSOD’s efficiency of scavenging superoxide a nion and its ability to resist high hydrostatic pressure by moderately reducing its stability.The above results indicated that MnSODs of deep-sea sea cucumber adapted to deep-sea environments through their amino acid changes in polarity,piezophilic behavior,and local stability.This study revealed the correlation between MnSOD and extreme environment,and will help improve our understanding of the organism’s adaptation mechanisms in deep sea.

Benthodytes occidentpalauta sp.nov.,a new species of deep-sea holothuroid(Elasipodida:Psychropotidae)from the west of Kyushu-Palau Ridge in the Western Pacific Ocean

Benthodytes occidentpalauta sp.nov.was collected from the Kyushu-Palau Ridge at a depth of 5481 m in 2021.This new species is characterized by a gelatinous body wall,violet skin,six pairs of dorsal papillae,and a rough mid-ventral surface without tube feet.The dorsal deposits are rod-shaped and tripartite.Two types of papillae deposits as crosses with four arms with central bipartite apophyses.Ventral deposits are rods.Tentacle ossicles are rod-shaped with end protrusions.Gonad deposits are rodshaped,tripartite,and cross-shaped.The phylogenetic analyses based on cytochrome oxidase subunit 1(COI)and 16S individually and a concatenated dataset of COI and 16S genes of this species support that B.occidentpalauta sp.nov.belongs to Benthodytes.

海参纲线粒体基因组特征分析及分子标记探讨

通过常规PCR和长PCR扩增获得仿刺参的线粒体DNA,进而采用鸟枪法测序、序列拼接获得仿刺参的线粒体基因组全序列。结合瓜参、拟刺参、海参及另外一个仿刺参的线粒体基因组,初步揭示了海参纲线粒体基因组的基本特征。楯手目的3个物种(仿刺参、拟刺参和海参)线粒体基因组的基因排列完全一致,且与海胆纲物种线粒体基因组的基因排列相同。隶属于枝手目的瓜参线粒体基因组的基因排列与其他海参线粒体基因组相比,发生6个tRNA基因的易位。海参纲线粒体基因组主编码基因的变异特征分析揭示了在海参类线粒体基因组所有的主编码基因中,cox1基因多态位点的比例最低,仅为29.46%;nad2、nad4、nad5三个基因的多态位点不仅比例较高,而且基因的长度较长,从而拥有最多的多态位点。因此,nad2、nad4和nad5基因可以cox1基因辅助的分子标记。

贵州独山早石炭世上司组海参化石

从贵州独山早石炭世上司组海参化石的发现,进一步讨论海参集合体的特点及其意义,海参化石组合特征,并与国内外石炭系海参进行对比,同时描述了上司组海参化石8属12种,包括5新种.

Benthodytes tetrapapillata sp.nov.,a new elasipodid sea cucumber(Elasipodida:Psychropotidae)from a seamount in the Western Pacific Ocean

Benthodytes tetrapapillata sp.nov.was collected from a seamount located on the Caroline Ridge at a depth of 2289 m,during the cruise of R/V Kexue in June 2019.We provided detailed descriptions of external and deposits morphology.The phylogenetic analyses based on cytochrome c oxidase I(COI)and a concatenated dataset of 16S and COI genes showed that the new species belonged to Benthodytes that is not monophyletic.Both details of morphological comparisons and molecular analyses confirmed that Benthodytes tetrapapillata sp.nov.is a new psychropotid species.A state of main morphological characters in valid species of Benthodytes is also provided in this study.

中国13种海参系统发育和骨片演化分析

运用扫描电子显微镜观察了中国沿海13种代表性海参的骨片,并获得了8种海参的线粒体16SrDNA基因序列,通过整合网上序列联合分析以期了解13种海参的系统发育关系和骨片演化规律。结果表明, 13种海参的骨片包括桌形体、假桌形体、扣状体、杆状体、穿孔板、花纹样体、颗粒体7种类型; 8种海参的16S rDNA片段长度在465 bp左右,富含AT碱基, A+T的含量平均为55.8%,符合无脊椎动物线粒体DNA序列的特征。从GenBank中获取11种海参16S rDNA基因序列,以杂色角孔海胆(Salmacis sphaeroides)为外群,联合本研究中所测序列构建了NJ和ME系统树。结果表明,NJ、ME系统发育树基本一致,海参科(Holothuriidae)内,柄体参属(Labidodemas)与海参属(Holothuria)亲缘关系极近且骨片形态均相似,可划分为同一个属;与传统形态学分类不同,刺参科(Stichopodidae)同尻参科(Caudinidae)、沙鸡子科(Phyllophoridae)、硬瓜参科(Sclerodactylidae)、瓜参科(Cucumariidae)聚成一簇,而与海参科亲缘关系较远,符合最新分类系统。本研究根据NJ和ME系统发育树结果,结合海参骨片的形态学资料,对海参科内骨片的演化进行了分析,认为虽然桌形体的进化史尚不清晰,但在海参科内,海参骨片由复杂的桌形体、扣状体向简单的花纹样体和颗粒体演化。

海参抗菌肽的活性筛选与功效评价

本文将已有文献报道的海洋动物源抗菌肽(毒素除外)与海参蛋白组进行比对,结合生物信息学软件,设计、筛选海参抗菌肽,并对其理化特性、抗菌活性与机制、生物相容性与细胞活性等进行研究。研究结果发现,通过软件模拟与抗菌活性预测,最终筛选并固相合成7条海参抗菌肽(H1-H7)。其中,H4(RVHRFLRR)可通过细菌膜电位去极化、膜透化等方式,抑制金黄色葡萄球菌(Staphylococcus aureus)、铜绿假单胞菌(Pseudomonas aeruginosa)、创伤弧菌(Vibrio vulnificus)生长,在较低浓度(31.25μg·mL^(-1))时,可使S.aureus细菌总数降至84.93%±4.21%(p<0.01),P.aeruginosa细菌总数降至95.92%±0.52%(p<0.01),V.vulnificus细菌总数降至77.14%±1.37%(p<0.01)。H4生物相容性好,在<1000μg·mL^(-1)时均未表现出溶血性或细胞毒性,其可能通过与细胞膜表面受体(EGFR、VEGFR2、FGFR1等)发生相互作用进而促进细胞迁移。在浓度为62.50μg·mL^(-1)和250μg·mL^(-1)时,H4均可显著促进L929细胞发生迁移(p<0.05)。实验结果表明,海参抗菌肽H4生物相容性好,兼有抗菌、促愈合功效,可望作为一种潜在功能物质用于感染创面的修复与再生。