بررسی مقایسه‏ ای ترنسکریپتوم برگ برنج تحت شرایط کنترل و تنش خشکی با استفاده از داده ‏های EST

نوع مقاله : علمی پژوهشی

نویسندگان

1 کارشناس بخش زیست شناسی سامانه ها، پژوهشکده بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی

2 استادیار بخش زیست شناسی سیستم‌ها، پژوهشکده بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی

3 استادیار، پژوهشکده بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج

4 دانشجوی دکترای کامپیوتر، دانشکده کامپیوتر، دانشگاه امیرکبیر، تهران

چکیده

برنج غذای اصلی بیش از نیمی از جمعیت جهان به ویژه کشورهای در حال توسعه است و خشکی مهمترین عامل کاهش عملکرد برنج در آسیا می‌باشد. این تحقیق به منظور شناسایی ژن‌های پاسخ دهنده به تنش خشکی با کمک تجزیه و تحلیل اطلاعات EST دو کتابخانه برگ برنج انجام شد. داده‌های کتابخانه‌های EST در شرایط شاهد و تنش خشکی، از پایگاه ‏داده NCBI دریافت و با استفاده از نرم‏افزار EGassembler ویرایش، دسته‏بندی و هم‏گذاری شدند. توالی‏های کانتیگ و سینگلتون به دست آمده به عنوان الگو برای جستجوی بلاست ‏x در بانک توالی پروتیین برنج و انتساب گروه عملکردی با استفاده از نرم‏ افزار CLC Genomic Workbench و AgriGO به کار برده شدند. پروتئین‌های شناسایی شده در کتابخانه‌های شاهد و خشکی به ترتیب در70 و 82 گروه کارکردی مختلف قرار گرفتند. برای شناسایی تفاوت‌های معنی‌دار بین گروه‌های کارکردی در کتابخانه‌های شاهد و تنش خشکی از نرم‏افزار IDEG6 استفاده شد. بررسی هستی‌شناسی ژن‌ها، تفاوت معنی‏‌دار در 20 گروه عملکردهای مولکولی، 35 گروه فرایندهای زیستی و 12 گروه اجزای درون سلول را آشکار ساخت. به منظور تعیین بیان افتراقی ژن‏ها بین دو کتابخانه، 4012 EST دارای کد Unigene با استفاده از الگوریتم پیاده‏ سازی شده در نرم‏افزار MATLAB انتخاب و با استفاده از نرم ‌افزار IDEG6 تفاوت معنی‌دار بین 42 ژن تحت تنش خشکی نسبت به شاهد، مشاهده شد (31 ژن افزایش و 11 ژن کاهش بیان). ژن‏های افزایش بیان یافته، در پاسخ به تنش‌های محیطی و اکسیداتیو، برقراری هموستازی، پروتئولیز و گلیکولیز نقش داشته و ژن‌های مربوط به فتوسنتز کاهش بیان نشان دادند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Comparative analysis of rice leaves transcriptome under control and drought stress conditions using EST data

نویسندگان [English]

  • Manzar Heidari 1
  • Zahra-Sadat Shobbar 2
  • Parisa Koobaz 3
  • Mohammad javad Heydari 4
1 Research assistant / Agricultural Biotechnology Research Institute Of Iran, Karaj
2 Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Education and Extension Organization (AREEO), Karaj, Iran.
3 Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Education and Extension Organization (AREEO), Karaj, Iran.
4 Ph.D. Student of Computer, Department of Computer and Information Technology, Amirkabir University of Technology, Tehran, Iran.
چکیده [English]

Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. EST libraries data under normal and drought stress conditions were downloaded from NCBI databank. Preprocessing, clustering and assembly of the EST sequences were done using EGassembler software. Generated contig and singleton sequences were used as template for BLASTx analysis against rice protein database and functional category assignment using CLC Protein Workbench software and AgriGO. The identified proteins in the normal and drought libraries were allocated to 70 and 82 functional categories, respectively. IDEG6 were used to identify significant differences between functional categories in control and drought stress libraries. Gene ontology analysis, revealed significant differences in 20 groups of molecular function, 35 groups of biological processes and 12 groups of the intracellular components. In order to find the significant differential expression between the two libraries, 4012 ESTs with unigene accession numbers were implemented through applying an algorithm by MATLAB software and were analyzed by IDEG6 software, where 42 genes were found to be differentially expressed between drought and normal conditions (31 up-regulated and 11 down-regulated genes). The up-regulated genes were involved in environmental and oxidative stress response, homestasis, proteolysis and glycolysis, while photosynthesis related genes were down-regulated.

کلیدواژه‌ها [English]

  • rice
  • Expressed Sequence Tag (EST)
  • Differentially expressed genes
  • Drought

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