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Bioinformatics Genome-Wide Characterization of the WRKY Gene Family in Sorghum bicolor | ||
Iranian Journal of Genetics and Plant Breeding | ||
مقاله 4، دوره 8، شماره 2 - شماره پیاپی 16، مرداد 2019، صفحه 33-45 اصل مقاله (2.06 M) | ||
نوع مقاله: Research paper | ||
شناسه دیجیتال (DOI): 10.30479/ijgpb.2020.12875.1266 | ||
نویسندگان | ||
Jafar Ahmadi* ؛ Kayvan Agahi؛ Sedigheh Fabriki Ourang | ||
Department of Genetics and Plant Breeding, Imam Khomeini International University, P. O. Box: 34148-96818, Qazvin, Iran. | ||
تاریخ دریافت: 19 اسفند 1398، تاریخ بازنگری: 31 فروردین 1399، تاریخ پذیرش: 03 اردیبهشت 1399 | ||
چکیده | ||
The WRKY gene family encodes a large group of transcription factors that regulate genes involved in plant response to biotic and abiotic stresses. Sorghum is a notable grain and forage crop in semi-arid regions because of its unusual tolerance against hot and dry environments. In this study, we performed a genome-wide analysis of WRKYs using a genome assembly of sorghum bicolor. First, all possible WRKY gene sequences as well as all possible WRKY protein sequences in the Sorghum bicolor genome database were identified using the NCBI website. A set of 85 WRKY genes was identified in the S. bicolor genome and classified into three groups (I–III). Among the members of the group I, the SbWRKY13 had a different and novel zinc finger motif as compared to other members of this group. It was also found that mutations occurred at R, K, Y and Q in the conserved WRKYGQK sequence. No complete gene duplication was found in gene copy number investigation, suggesting that the expansion of SbWRKY genes was not necessarily based on the gene duplication events or duplication of SbWRKY genes had probably happened in the past times. Gene cluster analysis showed that the number of genes on chromosomes were positively correlated with the number of clusters. The study of amino acid composition revealed that totally in all groups, Alanine and Proline were the most frequent residues while Cysteine had the lowest frequency. The study of introns in the SbWRKY domain showed that the majority of SbWRKY genes had two types of introns in their WRKY domains (phase 0 and phase 2). Also, investigation of conserved known motifs revealed that there were six, two and one known motifs outside of the region of the SbWRKY domain for groups IIa, IIb and IIc, respectively. The results describe evolution and functional differentiations of WRKY transcription factors in Sorghum bicolor. | ||
کلیدواژهها | ||
DNA-binding protein؛ Sorghum bicolor؛ Zing finger motif؛ WRKY | ||
عنوان مقاله [English] | ||
خصوصیات بیوانفورماتیکی خانواده ژنیWRKY درسورگوم | ||
نویسندگان [English] | ||
جعفر احمدی؛ کیوان آگاهی؛ صدیقه فابریکی اورنگ | ||
گروه مهندسی ژنتیک و بهنژادی گیاهی، دانشکده کشاورزی و منابع طبیعی، دانشگاه بین المللی امام خمینی (ره)، قزوین، ایران، کدپستی: 34148-96818. | ||
چکیده [English] | ||
خانوادة ژنی WRKYرمز کننده گروه بزرگی از فاکتورهای رونویسی هستند که فعالیت ژنهای مربوط به پاسخ گیاهان به تنشهای زنده و غیرزنده را تنظیم میکنند. سورگوم (Sorghum bicolor) به دلیل تحمل منحصربفرد در برابر محیطهای گرم و خشک، یک گیاه دانهای و علوفهای قابل توجه در مناطق نیمه خشک است. مجموعهای متشکل از 85 ژن WRKY در ژنوم S. bicolor شناسایی و در سه گروه (I-III) طبقهبندی شدند. در بین اعضای گروهI ،SbWRKY13 نسبت به سایر اعضای این گروه، از یک موتیف انگشت روی متفاوت و جدید برخوردار بود. نتایج نشان داد که جهش در جایگاههای R ،K ،Y وQ در توالی حفظ شدهWRKYGQK رخداده است. بررسی تعداد کپی ژنها نشان داد که هیچ تکثیر ژن کاملی پیدا نشد که نشان میدهد گسترش ژن SbWRKY لزوماً بر اساس وقایع تکثیر ژن اتفاق نیفتاده است و یا اینکه تکثیر ژنهای SbWRKY احتمالاً در زمانهای گذشته بوقوع پیوسته است. تجزیه و تحلیل خوشهای نشان داد که تعداد ژنهای روی کروموزومها با تعداد خوشههای ژنی ارتباط معنیدار دارد. بررسی ترکیب اسیدآمینه نشان داد که در کلیه گروهها، آلانین و پرولین فراوانترین اسیدهای آمینه بودند در حالی که سیستئین کمترین فراوانی را داشت. بررسی ساختار اینترونها نشان داد که اکثر ژنهای SbWRKY در حوزة WRKY خود دو نوع اینترون فاز 0 و فاز 2 را داشتند. همچنین بررسی موتیفهای حفاظت شده نشان داد که در گروههای IIa،IIb وIIc، شش موتیف شناخته شده در خارج از منطقة حوزة SbWRKY وجود داشت. نتایج تحقیق حاضر روند تکامل و تمایز عملکردی عوامل رونویسی WRKY را در سورگوم توصیف میکند. | ||
کلیدواژهها [English] | ||
پروتئینهای متصل شونده به DNA, سورگوم, موتیف انگشت روی, WRKY | ||
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