Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus.
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 degrees C over the next century.
Edmunds
Richard C
RC
Molecular Evolution and Ecology Laboratory, School of Marine & Tropical Biology, James Cook University, Townsville QLD 4811, Australia. richard.c.edmunds@gmail.com
van Herwerden
Lynne
L
Smith-Keune
Carolyn
C
Jerry
Dean R
DR
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D005091:Exons / Q000235:genetics; D007438:Introns / Q000235:genetics; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007770:L-Lactate Dehydrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010473:Perciformes / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment; D013696:Temperature
D007527:Isoenzymes; D035683:MicroRNAs; D007770:L-Lactate Dehydrogenase; C409667:lactate dehydrogenase 1