Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus
<p>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 (<i>Lates calcarifer</i> and <i>Lates niloticus</i>) we chara...
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| Format: | Article |
| Language: | English |
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Ivyspring International Publisher
2009-01-01
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| Series: | International Journal of Biological Sciences |
| Online Access: | http://www.biolsci.org/v05p0558.htm |
| _version_ | 1811192963878879232 |
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| author | Richard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry |
| author_facet | Richard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry |
| author_sort | Richard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry |
| collection | DOAJ |
| description | <p>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 (<i>Lates calcarifer</i> and <i>Lates niloticus</i>) we characterized both coding and non-coding regions of lactate dehydrogenase-B (<i>ldh-b</i>), a locus which exhibits temperature-adaptive differences among temperate and sub-tropical populations of the North American killifish <i>Fundulus heteroclitus</i>. <i>Ldh-b</i> was 5,004 and 3,527 bp in length in <i>L. calcarifer</i> and <i>L. niloticus</i>, 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 <i>ldh-b</i> (> 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 <i>Lates </i>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 <i>Lates </i>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.</p> |
| first_indexed | 2024-04-12T00:00:41Z |
| format | Article |
| id | doaj.art-6aa072a466aa4db3a1134f845cc7520d |
| institution | Directory Open Access Journal |
| issn | 1449-2288 |
| language | English |
| last_indexed | 2024-04-12T00:00:41Z |
| publishDate | 2009-01-01 |
| publisher | Ivyspring International Publisher |
| record_format | Article |
| series | International Journal of Biological Sciences |
| spelling | doaj.art-6aa072a466aa4db3a1134f845cc7520d2022-12-22T03:56:15ZengIvyspring International PublisherInternational Journal of Biological Sciences1449-22882009-01-0156558569Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticusRichard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry<p>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 (<i>Lates calcarifer</i> and <i>Lates niloticus</i>) we characterized both coding and non-coding regions of lactate dehydrogenase-B (<i>ldh-b</i>), a locus which exhibits temperature-adaptive differences among temperate and sub-tropical populations of the North American killifish <i>Fundulus heteroclitus</i>. <i>Ldh-b</i> was 5,004 and 3,527 bp in length in <i>L. calcarifer</i> and <i>L. niloticus</i>, 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 <i>ldh-b</i> (> 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 <i>Lates </i>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 <i>Lates </i>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.</p>http://www.biolsci.org/v05p0558.htm |
| spellingShingle | Richard C. Edmunds, Lynne van Herwerden, Carolyn Smith-Keune, Dean R. Jerry Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus International Journal of Biological Sciences |
| title | Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus |
| title_full | Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus |
| title_fullStr | Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus |
| title_full_unstemmed | Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus |
| title_short | Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus |
| title_sort | comparative characterization of a temperature responsive gene lactate dehydrogenase b ldh b in two congeneric tropical fish lates calcarifer and lates niloticus |
| url | http://www.biolsci.org/v05p0558.htm |
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