历史上的 "沉船":海军船虫 Teredo navalis Linnaeus 的转录组组装,1978 年

IF 1.3 4区 生物学 Q4 GENETICS & HEREDITY Marine genomics Pub Date : 2024-02-27 DOI:10.1016/j.margen.2024.101097
André Gomes-dos-Santos , Marcos Domingues , Raquel Ruivo , Elza Fonseca , Elsa Froufe , Diana Deyanova , João N. Franco , L. Filipe C. Castro
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引用次数: 0

摘要

软体动物船虫因其对人类建造的海洋木结构造成的负面影响而闻名于世,在海洋生态系统中发挥着核心的生态作用。它们与细菌共生体的结合提供了纤维素分解和固氮活动,突出了它们吃木头和钻木头的特殊行为,改善了能量传递和木纤维素中锁住的重要营养物质的循环。重要的是,从分子角度来看,这一双壳类动物谱系中存在大量的分子信息资源。在这里,我们制作并组装了分布于全球的海军舰船蠕虫(Teredo navalis,Teredinidae科)的转录组。该转录组是通过对海船虫标本全身五个等距节段的总 RNA 进行测序获得的。通过几种统计方法对所生成的组的质量进行了评估,结果表明这是一个高度连续(1194 N50)和完整(真核细胞和类元动物数据库的 BUSCO 分数超过 90%)的转录组,有近 38,000 个预测的 ORF,其中一半以上有功能注释。我们的发现为研究这些高度变异双壳类动物的独特进化生物学铺平了道路,并为该物种全基因组序列的充分基因注释奠定了基础。
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An historical “wreck”: A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978

Historically famous for their negative impact on human-built marine wood structures, mollusc shipworms play a central ecological role in marine ecosystems. Their association with bacterial symbionts, providing cellulolytic and nitrogen-fixing activities, underscores their exceptional wood-eating and wood-boring behaviours, improving energy transfer and the recycling of essential nutrients locked in the wood cellulose. Importantly, from a molecular standpoint, a minute of omic resources are available from this lineage of Bivalvia. Here, we produced and assembled a transcriptome from the globally distributed naval shipworm, Teredo navalis (family Teredinidae). The transcriptome was obtained by sequencing the total RNA from five equidistant segments of the whole body of a T. navalis specimen. The quality of the produced assembly was accessed with several statistics, revealing a highly contiguous (1194 N50) and complete (over 90% BUSCO scores for Eukaryote and Metazoan databases) transcriptome, with nearly 38,000 predicted ORF, more than half being functionally annotated. Our findings pave the way to investigate the unique evolutionary biology of these highly modified bivalves and lay the foundation for an adequate gene annotation of a full genome sequence of the species.

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来源期刊
Marine genomics
Marine genomics 生物-遗传学
CiteScore
3.60
自引率
5.30%
发文量
50
审稿时长
29 days
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.
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