تحلیل جامع ژنومی، تکاملی و ساختاری خانواده‌های ژنی دارای موتیف LysM در غلات

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرم آباد، ایران.

2 گروه مهندسی تولیدات گیاهی و ژنتیک، دانشکده کشاورزی، دانشگاه شهید چمران اهواز، اهواز، ایران.

3 مرکز تحقیقات تالاسمی و هموگلوبینوپاتی، پژوهشکده سلامت، دانشگاه علوم پزشکی جندی شاپور اهواز، اهواز، ایران.

چکیده

مقدمه: غلات منبع اصلی انرژی برای مصرف انسان و خوراک دام هستند. غلات در طول زندگی خود با تنش­های زنده و غیرزنده متعددی مواجهه می شوند که در بیشتر موارد به آنها خسارت وارد کرده و روی کیفیت و کمیت محصول آنها تاثیر می­گذارند. بنابراین، حفظ عملکرد آنها با جلوگیری از حمله پاتوژن­های بیمارگر به ویژه قارچ­ها و اوومیست­ها از اهمیت بالایی برخوردار است. پروتئین­های متعددی در مسیرهای سیگنالینگ مولکولی ویژه­ای در مقاومت غلات به تنش­ها دخالت دارند. در این میان، پروتئین‌های دارای موتیف لیزین(LysM)  نقش مهمی در ایمنی ذاتی گیاهان، روابط همزیستی بین گیاهان و میکروارگانیسم‌ها و بیوسنتز دیواره سلولی دارند. با این حال، مسیرهای تکاملی و تنوع عملکردی این خانواده از پروتئین‌ها برای مهمترین گیاهان زراعی بشر از جمله غلات به‌طور کامل ناشناخته باقی مانده است.
مواد و روش‌ها: در این مطالعه، یک تجزیه و تحلیل جامع ژنومی روی خانواده­های ژنی دارای موتیف LysM در هفت گونه اصلی غلات شامل: Avena sativa، Oryza sativa، Triticum aestivum، Sorghum bicolor، Hordeum vulgare، Zea mays و Secale cereale صورت گرفت. از ابزارهای بیوانفورماتیکی برای شناسایی ژن­ها و پروتئین‌های دارای موتیف لیزین (LysM) استفاده شد. غربالگری ژن­ها برای استخراج ژن­های هدف بر اساس نرم افزارهای مختلف و با توجه به پارامترهای پیش فرض، مشخص گردید.
یافته‌ها: در مجموع و در ژنوم این هفت غله، تعداد 106 ژن دارای موتیف LysM شناسایی شدند که در بین آنها، تنوع ساختاری قابل توجهی مشاهد شد و الگوهای پراکندگی کروموزومی متنوعی از خود نشان دادند. تجزیه و تحلیل­های فیلوژنتیکی، این ژن‌ها را به سه زیرخانواده‌ی مجزا طبقه‌بندی کرد که این موضوع نشان‌دهنده‌ی حفظ شدگی این پروتئین­ها در کنار روند تکامل اختصاصی آنها  است. تجزیه و تحلیل‌های بیشتر این ژن­ها، سینتنی (Synteny) و هم‌خطی (Collinearity) قابل توجهی را میان گونه‌های غلات نشان داد که بر محدودیت‌های تکاملی و حفظ عملکرد این خانواده از ژن­ها دلالت دارد. بررسی ساختار ژنی و تجزیه و تحلیل موتیف‌های حفاظت‌شده نیز بر تنوع عملکردی این ژن‌ها تأکید داشت. تجزیه و تحلیل عناصر تنظیمی Cis بیانگر نقش ژن‌های LysM در پاسخ به تنش‌های زیستی و غیرزیستی، به‌ویژه شناسایی عوامل بیماری‌زا و مسیرهای سیگنال‌دهی بود.
نتیجه‌گیری: یافته‌های این پژوهش، نشان دادند که ژن­های داری موتیف  LysMدارای پویایی تکاملی و اهمیت عملکردی در غلات هستند و از این رو، می­توان از آنها برای برنامه‌های اصلاح مولکولی غلات استفاده نمود. نتایج مطالعه حاضر، درک ما را از مکانیسم‌های مولکولی مبتنی بر ژن‌های داری موتیف  LysMو کاربردهای بالقوه‌ی آن‌ها در راهبردهای بهنژادی با هدف افزایش مقاومت به تنش و بهره‌وری در غلات را افزایش می‌دهد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Comprehensive Genomic, Evolutionary, and Structural Analysis of LysM Motif-Containing Genes in Cereals

نویسندگان [English]

  • رضایی میرقائد Rezaei Mirghayed 1
  • Farhad Nazarian-Firouzabadi 1
  • Seyyed Mohsen Sohrabi 2
  • Mohammad-Reza Mahmoudian-Sani 3
1 Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
2 Assistant professor, Production Engineering and Plant Genetics Department, Faculty of Agriculture, Shahid Chamran University, Ahvaz, Iran.
3 Assistant Professor of Thalassemia and Hemoglobinopathy Research Center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
چکیده [English]

Introduction: Cereals are the primary source of energy for human consumption as well as animal feed. Throughout their lifecycle, cereals are exposed to a wide range of both biotic and abiotic stresses that often lead to significant yield losses, impacting both the quality and quantity of their yield. Consequently, safeguarding their productivity, particularly by resistance against biotic threats such as fungi and oomycetes, is crucial. A variety of proteins play key roles in specialised molecular signalling pathways that enhance the stress resistance of cereals. To this end, maintaining cereal productivity by controlling plant diseases, particularly fungi and oomycetes, is of critical importance. LysM motif-containing proteins play significant roles in plant innate immunity, symbiotic interactions, plant-pathogen interactions, and cell wall biosynthesis. However, the evolutionary pathways and functional diversity of these protein families remain largely unknown in the major cereal crops.
Materials and methods: In this study, a comprehensive genomic analysis was conducted on LysM motif-containing gene families across seven major cereal species, including Avena sativa, Oryza sativa, Triticum aestivum, Sorghum bicolor, Hordeum vulgare, Zea mays, and Secale cereale. Bioinformatics tools were employed to detect genes and proteins featuring the lysin (LysM) motif. Target genes were selected through screening processes using multiple software platforms and predetermined parameters.
Results: A total of 106 LysM motif-containing genes were identified across seven selected cereal genomes. These genes exhibited considerable structural diversity and displayed a wide range of chromosomal distribution patterns. Phylogenetic analyses classified LysM motif-containing genes into three distinct subfamilies, indicating both evolutionary conservation and lineage-specific adaptations. Further analyses of LysM motif-containing genes revealed significant synteny and collinearity among the cereal species, suggesting evolutionary relationships and the functional conservation of LysM motif-containing genes. Gene structures and conserved motif analyses revealed the functional diversity of LysM motif-containing genes. Analysis of cis-regulatory elements indicated that LysM genes are involved in responses to both biotic and abiotic stresses, particularly in response to pathogen recognition and signalling pathways.
Conclusion: The findings of this study demonstrate that LysM motif-containing genes exhibit evolutionary dynamics and play important functional roles in cereals. Therefore, LysM motif-containing genes hold great potential in molecular breeding programs aimed at improving cereal crops to resist both biotic and abiotic stresses. The results of this study improve our understanding of the molecular mechanisms involving LysM motif-containing genes and highlight their potential applications in breeding strategies for improving stress resistance and productivity in cereals.

کلیدواژه‌ها [English]

  • Interaction
  • stress response
  • phylogenetic analysis
  • Chitin-binding domain
  • Systemic acquired resistance

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