Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

BMC Genomics

Research Article

A. Kristof¹  A. L. De Oliveira¹  M. Scherholz¹  T. Wollesen¹  E. Redl¹  A. Wanninger¹  C. Bleidorn²  C. Todt³ 

[1] Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria;Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain;Institute of Biology, University of Leipzig, 04103, Leipzig, Germany;University of Bergen, University Museum, The Natural History Collections, Allégaten 41, 5007, Bergen, Norway;

关键词: Bioinformatics;    EvoDevo;    Evolution;    Evolutionary developmental biology;    Genomics;    Mollusca;    Next-generation sequencing;    NGS;    Transcriptomics;    RNA-seq;   

DOI  :  10.1186/s12864-016-3080-9

 received in 2016-03-02, accepted in 2016-09-08,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa.ResultsNext-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks.ConclusionsThe use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.

【 授权许可】

CC BY   
© The Author(s). 2016