Idalyd Fonseca-González , Esteban Velasquez-Agudelo , Mario H. Londoño-Mesa , Javier C. Álvarez
{"title":"南极多毛目环节动物 Microspio moorei(匙吻鲟科)的全新转录组测序和注释及其热应激相关蛋白(HSP、SOD 和 CAT)的特征描述","authors":"Idalyd Fonseca-González , Esteban Velasquez-Agudelo , Mario H. Londoño-Mesa , Javier C. Álvarez","doi":"10.1016/j.margen.2024.101085","DOIUrl":null,"url":null,"abstract":"<div><p>We present a <em>de novo</em> transcriptome assembly for the non-model Antarctic polychaete worm <em>Microspio moorei</em> (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for <em>Microspio spp.</em> The gene sequences of the spionid worm were annotated from a wide range of functions (<em>i.e.</em>, biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the <em>Microspio</em> genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. Moreover, these results motivate the extension of these findings to congeneric species.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3000,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874778724000035/pdfft?md5=acd1b10e74769ae247fa80c6d3e833f3&pid=1-s2.0-S1874778724000035-main.pdf","citationCount":"0","resultStr":"{\"title\":\"De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT)\",\"authors\":\"Idalyd Fonseca-González , Esteban Velasquez-Agudelo , Mario H. Londoño-Mesa , Javier C. Álvarez\",\"doi\":\"10.1016/j.margen.2024.101085\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>We present a <em>de novo</em> transcriptome assembly for the non-model Antarctic polychaete worm <em>Microspio moorei</em> (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for <em>Microspio spp.</em> The gene sequences of the spionid worm were annotated from a wide range of functions (<em>i.e.</em>, biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the <em>Microspio</em> genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. 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De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT)
We present a de novo transcriptome assembly for the non-model Antarctic polychaete worm Microspio moorei (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for Microspio spp. The gene sequences of the spionid worm were annotated from a wide range of functions (i.e., biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the Microspio genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. Moreover, these results motivate the extension of these findings to congeneric species.
期刊介绍:
The journal publishes papers on all functional and evolutionary aspects of genes, chromatin, chromosomes and (meta)genomes of marine (and freshwater) organisms. It deals with new genome-enabled insights into the broader framework of environmental science. Topics within the scope of this journal include:
• Population genomics and ecology
• Evolutionary and developmental genomics
• Comparative genomics
• Metagenomics
• Environmental genomics
• Systems biology
More specific topics include: geographic and phylogenomic characterization of aquatic organisms, metabolic capacities and pathways of organisms and communities, biogeochemical cycles, genomics and integrative approaches applied to microbial ecology including (meta)transcriptomics and (meta)proteomics, tracking of infectious diseases, environmental stress, global climate change and ecosystem modelling.