| 摘要: |
| 劳盆拟刺铠虾(Munidopsis lauensis)是一种十足目铠甲虾, 能够适应深海化能合成生态系统的极端环境, 但是其已知基因序列信息却很少。为此, 采用PacBio平台的SMRT测序技术对来自南海台西南冷泉劳盆拟刺铠虾的肝胰腺、鳃、肌肉和肠混合组织进行了三代全长转录组测序。通过聚类、校正、去冗余之后共获得28 811条高质量isoform, 平均长度为2 086 bp, N50长度为2 275 bp。使用Nr、SwissPort、KEGG、KOG数据库对转录本序列进行功能注释, 共有20 616 (71.56%)条isoform得到注释。进一步高级注释共获得21 848个蛋白编码序列, 共预测到537个转录因子、6 430个长链非编码RNA和10 060个SSRs位点。KEGG通路分析发现两条可能与劳盆拟刺铠虾适应深海化能极端生境相关的通路, 分别为过氧化物酶体通路和谷胱甘肽代谢通路。其中, 共有180条isoform被发现参与编码过氧化物酶体通路中的31个关键酶, 213条isoform参与谷胱甘肽代谢通路中19个关键酶的编码。基于全长转录组数据, 利用同源比对、功能结构域预测及系统发育树构建等方法对劳盆拟刺铠虾谷胱甘肽S-转移酶(GST)基因家族进行挖掘与鉴定, 共发现属于theta、delta、mu、kappa四种亚家族的20条GST候选序列。通过对劳盆拟刺铠虾全长转录组测序、功能注释和环境适应相关的重要基因及通路的分析, 不仅丰富了深海组学数据资源, 也为进一步揭示甲壳动物适应深海化能极端环境的分子机制奠定了基础。 |
| 关键词: 劳盆拟刺铠虾 深海化能生态系统 全长转录组 功能注释 极端环境适应 |
| DOI：10.11693/hyhz20230300058 |
| 分类号: |
| 基金项目:中国科学院战略性先导科技专项,XDB42000000号,XDA22050302号;国家自然科学基金项目,42025603号。 |
附件 |
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| SMRT SEQUENCING OF FULL-LENGTH TRANSCRIPTOME OF THE MUNIDOPSID SQUAT LOBSTER MUNIDOPSIS LAUENSIS ENDEMIC TO DEEP-SEA CHEMOSYNTHETIC ENVIRONMENTS |
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YAN Han1,2, HUI Min1,3, SHA Zhong-Li1,3, CHENG Jiao1,3
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1.Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;2.University of Chinese Academy of Sciences, Beijing 100049, China;3.Laoshan Laboratory, Qingdao 266237, China
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| Abstract: |
| The munidopsid squat lobster Munidopsis lauensis (Baba and de Saint Laurent, 1992) is endemic to deep-sea chemosynthetic environments. However, no reference genome or transcriptome is available for M. lauensis, which impedes the studies of evolution and adaptation studies of the species. Therefore, we aimed to obtain the full-length (FL) transcriptome of M. lauensis using PacBio single molecule real-time sequencing (SMRT) technology. The total RNA extracted from hepatopancreas, gill, muscle, and intestinal tract of the species was mixed for SMRT sequencing. After isoform-level clustering, polishing, and redundancy removing, we identified 28 811 high-quality isoforms with mean length value of 2 086 bp and N50 value of 2 275 bp. A total of 20 616 (71.56%) isoforms had at least one significant hit in the Nr, SwissProt, KOG, or KEGG databases. We further predicted 21 848 coding sequences, 537 transcription factors, 6 430 long non-coding RNAs and 10 060 simple sequence repeats. Two pathways possibly associated with deep-sea extreme environment adaptation in M. lauensis were identified, including Peroxisome pathway with 31 key enzymes encoded by 180 isoforms and Glutathione metabolism pathway with 19 key enzymes encoded by 213 isoforms. A total of 20 GST-encoding isoforms, belonging to four GST classes (theta, delta, mu, and kappa), were identified from M. lauensis FL transcriptome by examining multiple-sequence alignments for conserved functional domains and by performing phylogenetic analyses. Overall, this study provided the first large-scale FL transcriptome in M. lauensis, allowing for functional, structural, and genomics studies of this endemic crustacean species found in deep-sea chemosynthetic ecosystems, and enriched the data resources of deep-sea genomics for further studies on molecular mechanisms of deep-sea extreme environment adaptation in crustaceans. |
| Key words: Munidopsis lauensis deep-sea chemosynthetic ecosystem full-length transcriptome functional annotation extreme environment adaptation |
