Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome

Abstract

As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates.

Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

“…The assembly using combined 454 and SOLiD data generated 53,862 contigs, which were then merged with 22,322 NCBI EST sequences and 81,479 sequences from a 454-based Asian seabass intestine assembly published earlier [9], resulting in 157,457 contigs. A co-assembly of these contigs with the previously reported HiSeq Round 1 (HR1) assembly [7] resulted in 362,369 contigs. Since we observed the presence of contigs, which were identical except for short terminal overhangs, we performed a sequence clustering using cd-hit-est to retain only the longest representative for highly similar contigs, resulting in a polished "Multiplatform" (MP) dataset of 196,871 contigs ( Figure 1, Table 2).…”

“…The 454 and SOLiD sequence datasets were first co-assembled, and later merged with Asian seabass ESTs from NCBI and a 454-based Asian seabass intestine assembly [9]. These sequences were then merged with a previous version of the Asian seabass transcriptome from the first round of HiSeq data [7] to produce a "multiplatform" assembly, which was further polished to remove low-coverage and redundant sequences. Independently, the second round of HiSeq data was assembled (library-wise) using Trinity, and then clustered to remove redundancies.…”

“…The 454 and SOLiD sequence data (incorporated and reassembled here) has been published and released previously [8]. The assembly from the initial round of Illumina HiSeq sequencing (HiSeq Round 1, HR1) was also utilized as part of a survey of repetitive elements in Asian seabass [7].…”

“…Our publication adds to the growing number of NGS-based transcriptome studies on the Asian seabass [7][8][9], and that of other food fishes such as Atlantic salmon (Salmo salar [10]), common carp (Cyprinus carpio [11]), European seabass (Dicentrarchus labrax [12,13]), rainbow trout (Oncorhynchus mykiss [14]), turbot (Scophthalmus maximus [15]), and striped bass (Morone saxatilis [16]). …”

“…The genome of the Asian seabass is estimated to be ~700 Mb and is currently being assembled and annotated [5], while the mitochondrial genome has previously been completely sequenced [6]. Transcriptome information for the Asian seabass to date is mainly represented by ~22,000 EST sequences in GenBank along with a limited number of organ-specific transcriptome studies and repetitive sequence analyses [7][8][9].…”