Comparative characterization of a temperature responsive gene (lactatedehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus

Edmunds, Richard C., van Herwerden, Lynne, Smith-Keune, Carolyn, and Jerry, Dean R. (2009) Comparative characterization of a temperature responsive gene (lactatedehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus. International Journal of Biological Sciences, 5 (6). pp. 558-569.

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The characterization of candidate loci is a critical step in obtaining insight into adaptation and acclimation of organisms. In this study of two non-model tropical (to sub-tropical) congeneric perciformes (Lates calcarifer and Lates niloticus) we characterized both coding and non-coding regions of lactate dehydrogenase-B (ldh-b), a locus which exhibits temperature-adaptive differences among temperate and sub-tropical populations of the North American killifish Fundulus heteroclitus. Ldh-b was 5,004 and 3,527 bp in length in L. calcarifer and L. niloticus, respectively, with coding regions comprising 1,005 bp in both species. A high level of sequence homology existed between species for both coding and non-coding regions of ldh-b (> 97% homology), corresponding to a 98.5% amino acid sequence homology. All six known functional sites within the encoded protein sequence (LDH-B) were conserved between the two Lates species. Ten simple sequence repeat (SSR) motifs (mono-, di-, tri- and tetranucleotide) and thirty putative microRNA elements (miRNAs) were identified within introns 1, 2, 5 and 6 of both Lates species. Five single nucleotide polymorphisms (SNPs) were also identified within miRNA containing intron regions. Such SNPs are implicated in several complex human conditions and/or diseases (as demonstrated by extensive genome-wide association studies). This novel characterization serves as a platform to further examine how non-model species may respond to changes in their native temperatures, which are expected to increase by up to 6°C over the next century.

Item ID: 49594
Item Type: Article (Research - C1)
ISSN: 1449-2288
Keywords: Barramundi, Nile perch, exons, introns, microRNAs, SSRs
Funders: James Cook University Research Advancement Program (JCU)
Date Deposited: 18 Jul 2017 22:24
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060409 Molecular Evolution @ 50%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060306 Evolutionary Impacts of Climate Change @ 50%
SEO Codes: 96 ENVIRONMENT > 9603 Climate and Climate Change > 960305 Ecosystem Adaptation to Climate Change @ 100%
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