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Title: Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome
Authors: Kuznetsova, Inna S.
Thevasagayam, Natascha M.
Sridatta, Prakki S. R.
Komissarov, Aleksey S.
Saju, Jolly M.
Ngoh, Si Y.
Jiang, Junhui
Shen, Xueyan
Orbán, László
Keywords: DRNTU::Science::Biological sciences::Genetics
Issue Date: 2014
Source: Kuznetsova, I. S., Thevasagayam, N. M., Sridatta, P. S. R., Komissarov, A. S., Saju, J. M., Ngoh, S. Y., et al. (2014). Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome. Frontiers in Genetics, 5.
Series/Report no.: Frontiers in Genetics
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.
ISSN: 1664-8021
DOI: 10.3389/fgene.2014.00223
Schools: School of Biological Sciences 
Rights: © 2014 Kuznetsova, Thevasagayam, Sridatta, Komissarov, Saju, Ngoh, Jiang, Shen and Orbán. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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