Analyzing Simple Sequence Repeats Derived from Expressed Sequence Tags in Dromedary Camels
Subject Areas : Camelا. برازنده 1 * , م. مختاری 2 , م. مقبلی دامنه 3 , ز. رودباری 4
1 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
2 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
3 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
4 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
Keywords: camel, SSR, Molecular marker, genomic, EST, gene ontology,
Abstract :
The objective of the current research was to make a character description of simple sequence repeats (SSR) derived from expressed sequence TAGs (EST) markers of dromedary camels (EST-SSR markers) and to conduct a practical analysis of these sequences for their application in comparative genomics and molecular genetics studies. A complete of 862 SSRs were discovered from 17155 EST sequences using the SSR Locator software. 827 EST out of 17155 EST had SSRs, that 794 (96%), 31 (3.8%) and 2 (0.2%) of them contained 1, 2 and 3 SSRs, respectively. The dimeric motifs were the most abundant SSRs (38.86%), followed by 27.15%, 21.46%, 6.96%, and 5.57% for tri-, hexa-, tetra- and pentameric motifs. The most plentiful dimer, trimer, tetramer, pentamer and hexamer motif were AC/TG (54%), GCC/GGC (19.2%), TTTA (13.3%), AAAAG (10.4%) and AACCAC (67.6 %), respectively. BLASTX was used to examine the final non-redundant EST-SSRs. Almost all of EST-SSRs were found out to be protected in the macromolecule catabolic process and RNA processing and splicing. EST-SSR markers might be applied as a novel resource of useful markers in the biological survey. Also, these markers may be a valuable source for further molecular genetics and genomics research of camels and related species.
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