Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3080-9) contains supplementary material, which is available to authorized users.

A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

“…rubrolineata (Lischke, 1873) (KY827039 [55];) and Ischnochiton hakodadensis Carpenter, 1893 (KY827038 [56]; ). We further assembled transcriptomes from four available chiton RNAseq datasets: Acanthochitona crinita (Pennant, 1777) (SRR5110525; [57]), Leptochiton rugatus (Carpenter in Pilsbry, 1892) (SRR1611558 [58];), Chiton (Rhyssoplax) olivaceus Spengler, 1797 (SRR618506 [59];), and Tonicella lineata (Wood, 1815) (SRR6926331 [60];). Transcriptomes were assembled de novo using Trinity v.2.8.2 and protein-coding and rRNA genes were identified by homology search against available chiton mitogenomes using BLAST [61].…”

The evolution of molluscs

“…Recent advances in palaeontological, phylogenetic, developmental, and experimental approaches have revealed some of the mysteries revolving around the emergence of the large phenotypic diversity encountered in modern and fossil species. The recent establishment of genomic editing tools such as the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats‐associated protein) system in molluscs (Perry & Henry, ), together with the ever‐increasing genomic (Zhang et al, ; Simakov et al, ; Albertin et al, ; Li et al, ; Wang et al, ) and transcriptomic resources (De Oliveira et al, ; Li et al, ), provide an ideal base to finally pursue questions concerned with molluscan functional genetics. To this end, some molluscan species have already been demonstrated to be particularly amenable to becoming true laboratory models, including the gastropods Ilyanassa obsoleta (Goulding & Lambert, ) and Crepidula fornicata (Henry & Lyons, ).…”

Gonad transcriptome of golden musselLimnoperna fortuneireveals potential sex differentiation genes

“…Assembled contigs completeness assessment by the representation of 978 core metazoan genes using BUSCO found 99.3% complete recovered genes for the final L. fortunei transcriptome, which is the highest percentage found for completeness of a transcriptome assembly in bivalves (47)(48)(49)(50)(51)(52)(53). Additionally, 87.94% of the clean RNA-seq reads were successfully mapped back to the assembled transcriptome, showing most of the reads being represented in the final assembly.…”