Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

海绵在诸多海洋与淡水生境中可成为优势类群，发挥着不可或缺的生态功能。同时，海绵也是探究早期后生动物（Metazoa）演化重大科学问题的关键类群。近年来，旨在深化海绵生物与生态功能认知、乃至解析动物演化机制的研究思路，多聚焦于参与环境变化（生物与非生物因子）响应、发育及繁殖过程的遗传工具箱。这类研究得以推进，得益于新兴的大规模测序技术——例如Illumina测序平台，其可实现兼具成本效益的基因组与转录组测序。本研究首次采用二代测序（next-generation sequencing, NGS）技术，解析一种附生海洋海绵的生活周期。为此，我们对地中海优雅绵（Crella elegans）的三个不同生活周期阶段的文库进行测序，并开展从头转录组组装。其中三个组装分别基于单个生活周期阶段的海绵组织，具体包括非繁殖组织、携带精子囊的组织以及携带幼虫的组织。第四个组装则整合了上述三个阶段的全部测序数据。相较于单阶段组装，通过整合所有不同生活周期阶段的数据，我们获得的重叠群（contig）总数、具有BLAST比对结果的重叠群数目以及经注释的重叠群数目均更高。相较于其他所有组装类型，该多阶段组装获得了更多已知的后生动物发育调控基因。此外，我们还针对三个生活周期阶段中的候选基因开展差异表达分析，以探究RNA-seq技术在深化海绵生活周期功能过程认知方面的应用潜力。