Transcriptome Sequencing of Guilan Native Cow in Comparison with bosTau4 Reference Genome
محورهای موضوعی : Camel
م. مریدی
1
(Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran)
س.ح. حسینی‌مقدم
2
(Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran)
س.ض. میرحسینی
3
(Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran)
کلید واژه: cDNA library, Guilan native cattle, Illumina Hiseq 2000, RNA-sequencing,
چکیده مقاله :
RNA-sequencing is a new method of transcriptome characterization of organisms. Based on identity and relatedness, there are large genetic variations among different cattle breeds. The goal of the current study was to sequence the transcriptome of Guilan native cow and compare with available reference genome using RNA-sequencing method. Blood samples were collected from 14 Guilan native cows and then were pooled with same ratios of 3 micrograms per sample. Sequencing of the pooled sample was carried out using Illumina Hiseq 2000 from both end and 100 base pair of reading length. Tophat2 software was used to align the reads with reference genome and identify splice junctions and insertions and deletions. Cufflinks software was used to assemble transcripts and calculate their abundances. Total numbers of sequenced RNA fragments were 28434708 and the overall reading map was 87.4 percent. Total numbers of expressed genes were 24616 genes, which 19994 genes from these were protein coding genes and 3825 genes were non-coding. Adenosine triphosphate synthase 6 (ATP6) and ribosomal protein, large, P1 (RPLP1) genes showed the highest abundances of all expressed genes. The majority of highly expressed genes were involved in ribosomal structures and translational activities; moreover, they were belonging to housekeeping genes. The current study is a report of leukocytes transcriptome sequencing of Guilan native cow which have been not reported, so far. As Guilan native cow has the biggest population among all native populations in Iran, such studies could help to evaluate the genetic potential of this high precise genetic resource in Western Asia.
تعیین توالی RNA روش جدید تعیین خصوصیات ترانسکریپتوم موجودات زنده می­باشد. با در نظر گرفتن ماهیت نژادی و ارتباطات خویشاوندی، تنوع ژنتیکی گسترده­ای بین نژادهای مختلف گاو وجود دارد. هدف از مطالعه حاضر تعیین توالی ترانسکریپتوم گاو بومی گیلان و مقایسه آن با ژنوم مرجع موجود با استفاده از روش RNA-sequencing می­باشد. نمونه­های خون از 14 رأس گاو بومی گیلان جمع­آوری و با نسبت مشابه 3 میکروگرم به ازاء هر نمونه با یکدیگر ادغام شدند. توالی‌یابی نمونه ادغام شده توسط دستگاه Illumina Hiseq 2000 از هر دو جهت و با طول خوانش 100 جفت بازی انجام شد. از نرم­افزار TopHat2 جهت هم‌تراز کردن خوانش­ها با ژنوم مرجع و تشخیص جایگاه­های برش، حذف و اضافه­ توالی استفاده شد. از نرم­افزار Cufflinks جهت سرهم کردن ترانسکریپت­ها و محاسبه فراوانی آنها استفاده شد. تعداد کل قطعات RNA تعیین توالی شده 28434708 و نرخ کلی تطابق با ژنوم مرجع 4/87 درصد بدست آمد. تعداد کل ژن‌های بیان شده 24616 ژن بود که از این بین تعداد 19994 ژن کد کننده پروتئین و 3825 ژن غیر کد کننده پروتئین بودند. ژن‌های ATP6 (آدنوزین تری فسفات سنتاز 6) و RPLP1 (پروتئین ریبوزومی، بزرگ، P1) بالاترین فراوانی را در تمامی ژن‌های بیان شده نشان دادند. اکثریت ژن‌های دارای بیان بالا در ساختار ریبوزومی و فعالیت­های ترجمه دخالت داشتند که به عنوان ژن‌های خانه­دار در نظر گرفته می­شوند. مطالعه حاضر گزارشی از تعیین توالی ترانسکریپتوم گاو بومی گیلان می­باشد که تا به حال گزارش نشده است. با توجه به این که گاو بومی گیلان بزرگ­ترین جمعیت را در میان جمعیت­های گاو بومی ایران دارا میباشد، این قبیل مطالعات می­توانند به ارزیابی پتانسیل ژنتیکی این ذخیره ژنتیکی با ارزش در ناحیه غرب آسیا کمک کند.
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