Analyzing Simple Sequence Repeats Derived from Expressed Sequence Tags in Dromedary Camels
محورهای موضوعی : Camel
ا. برازنده
1
(
Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
)
م. مختاری
2
(
Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
)
م. مقبلی دامنه
3
(
Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
)
ز. رودباری
4
(
Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
)
کلید واژه: camel, SSR, Molecular marker, genomic, EST, gene ontology,
چکیده مقاله :
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.
هدف از تحقیق حاضر بررسی ویژگی های توالی های تکراری ساده مشتق شده از توالی های بیان شده برچسب دار (نشانگرهای EST-SSR) در شتر تک کوهانه و همچنین تجزیه و تحلیل عملکردی این نشانگرها جهت استفاده در مطالعات مولکولی و ژنومی بود. از 17155 توالی EST با استفاده از نرم افزارSSR Locator تعداد 862 توالی تکراری ساده (SSRs) بدست آمد. به طورکلی تعداد 827 توالی EST دارای SSR بوده که 794 (96 درصد)، 31 (8/3 درصد) و 2 (2/0 درصد) تا از آنها به ترتیب حاوی 1، 2 و 3 توالی SSR بودند. موتیفهای دایمری فراوانترین نوع SSR بودند و پس از آنها به ترتیب موتیفهای تری، هگزا، تترا و پنتامری با 27.15، 21.46، 6.96 و 5.57 درصد قرار گرفتند. فراوانترین موتیف های دایمر، تریمر، تترامر، پنتامر و هگزامر به ترتیب AC/TG (54 درصد)، GCC/GGC (19.2 درصد)، TTTA (13.3 درصد)، AAAAG (10.4 درصد) و AACCAC (67.6 درصد) بودند. نشانگرهای EST-SSR نهایی با استفاده از BLASTX بررسی شدند. تقریباً اکثر این نشانگرها در فرایندهای کاتابولیک ماکرومولکول ها و پردازش و اسپلایسینگ RNA مشارکت داشتند. میتوان از نشانگرهای EST-SSR به عنوان نشانگرهای جدید مفید در بررسیهای بیولوژیکی استفاده نمود. همچنین این نشانگرها یک منبع ارزشمند جهت مطالعات مولکولی و ژنومی شتر و گونه های مرتبط با آن هستند.
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