Pyrosequencing of Haliotis diversicolor Transcriptomes: Insights into Early Developmental Molluscan Gene Expression

Abstract

BackgroundThe abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking.Methodology/Principal FindingsIn this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the ‘lock system’ in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae.ConclusionThis study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.

Deep mRNA Sequencing of the Tritonia diomedea Brain Transcriptome Provides Access to Gene Homologues for Neuronal Excitability, Synaptic Transmission and Peptidergic Signalling

“…A BLAST comparison with RefSeq and SwissProt protein databases, as well as with mRNA/TSA sequences from other invertebrates indicates that the assembly contains a vast amount of genetic information, with more than 18,000 unigene sequences finding strong homology in the other databases. Gene ontology mapping corroborates a diversity of gene content and produces a strikingly similar GO term distribution as other molluscan transcriptomes [5,7,12,13]. The Tritonia TSA contains a vast number of transcripts with full to nearly full-length protein coding sequences, allowing for the extraction of Tritonia gene homologues that underlie neuronal excitability, synaptic transmission, and neuropeptide secretion.…”

“…Interestingly, level 2 filtering of GO terms produced a distribution remarkably similar to those of fellow molluscs derived using a diversity of different sequencing technologies: Lymnaea stagnalis (Illumina sequencing of CNS [7]), Aplysia californica (Sanger sequencing of CNS [5]), Octopus vulgaris (Illumina sequencing of CNS [12]) and Haliotis diversicolor (Roche 454 sequencing of larvae [13]) (S2 Fig.). This makes sense, given that the GO term distributions are relative and would scale proportionately regardless of gene sequence number.…”

De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome

“…Rather than carrying out separate transcriptome assemblies for each life stage, Illumina sequences from both experiments were combined and assembled into a single transcriptome, allowing generation of a more complete transcriptomic resource, and direct comparison of larvae and adults. This data provides an invaluable resource for identifying transcripts involved in the response of H. tuberculata to global change and other anthropogenic stresses, and taken with other recent high throughput transcriptomic data for Haliotis species (De Wit and Palumbi, 2013;Franchini et al, 2011;Huang et al, 2012;Picone et al, 2015;Shiel et al, 2015;Valenzuela-Muñoz et al, 2014) enriches the genomic resources available for this commercially important genus.…”

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai

“…Genes involved in numerous metabolic pathways such as innate immunity, cell stress and repair system, and antioxidant defense systems have been cloned and tested to determine their mRNA expression, translational inducibility, and molecular functions. Recently, the use of a genomics platform was successfully applied in H. discus hannai , although many research groups have continuously employed ‘-omics’ platforms (e.g., genomics, proteomics, linkage map development, Bacterial Artificial Chromosome (BAC) library construction) to understand the growth, development, reproduction, molecular adaptation, or innate immune response mechanisms upon environmental stressors or pathogen challenges in the Haliotis genus [5,6,7,8,9,10,11,12,13,14]. For H. discus hannai , a genetic linkage map was constructed as a potential application of marker-assisted selection in breeding programs using amplified fragment length polymorphism (AFLP) markers [15].…”