بازسازی شبکه‌های ژنی و پروتئینی پاسخ به تنش شوری در آفتابگردان (Helianthus annus L.) به وسیله داده‌های RNA-seq

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه زراعت و اصلاح نباتات، دانشکده علوم و مهندسی کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران

2 گروه زراعت و اصلاح نباتات، دانشکده علوم و مهندسی کشاورزی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران.

3 استاد، گروه اصلاح و بیوتکنولوژی گیاهی، دانشگاه ارومیه، ارومیه و استاد، پژوهشکده زیست‌فناوری دانشگاه ارومیه، ارومیه.

4 گروه تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران.

چکیده

هدف: آفتابگردان با تامین 12 درصد از روغن‌های گیاهی جهان یکی از مهم‌ترین گیاهان روغنی جهان محسوب می­شود. با توجه به پیچیدگی مولکولی مکانیسم پاسخ به تنش شوری که باعث تغییرات فیزیولوژیک، مورفولوژیک در گیاهان می­شود و همچنین حساسیت نسبی آفتابگردان به این تنش، هدف از این تحقیق درک مکانیسم‌های مولکولی و شناسایی پروتئین­های دخیل در تحمل به شوری در آفتابگردان می­باشد.
مواد و روش‌ها: در تحقیق حاضر، داده‌های RNA-seq از پژوهش Sharifi و همکاران (2022) استخراج و با بهره‌گیری از نرم‌افزارهای FastQC و Trimmomatic ویرایش گردیدند. پس از آن، آنالیز RNA-seq با دو روش سرهم‌بندی نو پدید و مبتنی بر ژنوم‌ انجام شد. خوانش‌ها به کمک پکیج Bowtie2 به ترنسکریپتوم مرجع و با Hisat2 به ژنوم مرجع نقشه‌یابی شدند. کمی‌سازی خوانش‌ها توسط RSEM و HT-seq و تغییرات در بیان ژن‌ها با استفاده از edgeR و DE-seq2 محاسبه گردید. ژن‌های دارای بیان متفاوت معنی‌دار (DEG) در آرابیدوپسیس شناسایی شده و برای بازسازی شبکه‌های تعامل پروتئینی (PPI) و شبکه‌های تنظیمی ژنی (GRN) به پایگاه‌های داده STRING و GeneMANIA وارد شدند. تحلیل توپولوژی این شبکه‌ها با 11 الگوریتم Cytohubba در Cytoscape انجام و ژن‌های هاب شناسایی گردیدند. توالی راه‌انداز این ژن‌ها در Plantcare مورد بررسی قرار گرفت. در پایان، بیان ژن COP1 با استفاده از Real-time PCR ارزیابی شد.
نتایج: تحلیل RNA-seq با استفاده از روش‌های مبتنی بر سرهم‌بندی نو پدید (دی نوو) و مبتنی بر ژنوم مرجع، به شناسایی 1602 رونوشت و 272 ژن با الگوی بیان متفاوت انجامید. مطالعه بر روی شبکه‌های GRN و PPI منجر به کشف 29 ژن هاب گردید که شامل BAK1، ETR1، GER3، HSP70، CDKB2;2، CAS، GRDP1، BSL3، CPN20، AOR، MCM7، DXS، AdoMet-MTases، RCA، P45090C1، C3H37، CDPK6، Lac1، WRKY50، COP1، PP2C76، CaM-7، Histone H1-3، PPR، LRR-RLK، LACS، LUT5 و Clp5 هستند که در فرآیندهای کلیدی سلولی از جمله تنظیم هورمون‌های گیاهی (ABA، BR، اتیلن)، پیام‌رسانی MAPK، پردازش RNA، فتوسنتز، تنظیم روزنه‌ها، حفظ ساختار پروتئین‌ها و چرخه سلولی نقش ایفا می‌کنند. تحلیل راه‌انداز این ژن‌ها وجود موتیف‌های کلیدی مانند W-box، TGA-box، ERE، ABRE، MYC، MYB، MBSI، MBS و GT-1motif را که نشان‌دهنده نقش مشترک آن‌ها در واکنش به شوری است را تأیید کرد. در نتایج حاصل از PCR زمان واقعی برای ژن COP1، که یکی از ژن‌های فعال در مسیر علامت­دهی ABA به شمار می‌رود، الگوی بیان آزمایش شده با الگوی مشخص شده توسط RNA-seq همخوانی داشت.
 نتیجه‌گیری: پژوهش حاضر با استفاده از رویکرد زیست‌شناسی سامانه‌ای نشان داد که آفتابگردان در واکنش به تنش نمکی، فعالیت ژن‌ها را در مسیرهای کلیدی سلولی از جمله مسیرهای پیام‌رسانی هورمونی گیاهی (ABA، BR، اتیلن)، مسیر MAPK، پردازش RNA، فتوسنتز، تنظیم روزنه‌ها، حفظ ساختار پروتئین‌ها و چرخه سلولی، بهینه‌سازی می‌کند. این نتایج، فهم ما از مکانیسم‌های مولکولی تحمل به شوری را تقویت کرده و می‌تواند در بهبود ژنتیکی آفتابگردان به منظور افزایش مقاومت در برابر شوری مفید واقع شود.

کلیدواژه‌ها

عنوان مقاله [English]

Reconstruction of Gene and Protein Networks in Response to Salt Stress in Sunflower (Helianthus annus L.) Using RNA-seq Data

نویسندگان [English]

  • Omid Mohammadalizadeh 1
  • Valliollah Mohammadi 2
  • Reza Darvishzadeh 3
  • Masoumeh Sharifi Alishah 4
1 Department of Agronomy & Plant Breeding, Faculty of Agronomy Sciences, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran.
2 Department of Agronomy & Plant breeding, Faculty of Agronomy Sciences, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran.
3 Professor, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran and Institute of Biotechnology, Urmia University, Urmia, Iran
4 Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
چکیده [English]

Objective
Sunflower is one of the most important oilseed products in the world, providing 12% of vegetable oils. Due to the molecular complexity involved in salt stress and its role to physiological and morphological changes in plants, as well as the moderate sensitivity of sunflower to this problem, the purpose of this work is elucidating with priority what affect on the proteins level has a cause-and-effect relationship with tolerance mechanisms.
Materials and methods
FastQC and Trimmomatic were used to process RNA-seq data that was taken from the study by Sharifi et al., (2022). RNA-seq analysis was then carried out using genome-based and de novo assembly techniques. Bowtie2 and Hisat2 were used to map the reads to the reference transcriptome and genome, respectively. RSEM and HT-seq were used to quantify the reads, and edgeR and DE-seq2 were used to identify differentially expressed genes (DEGs). Using the STRING and GeneMANIA databases, DEGs in Arabidopsis were found and incorporated into the Gene Regulatory Networks (GRN) and Protein-Protein Interaction (PPI) networks. Topological analysis of these networks was conducted using 11 algorithms in Cytohubba on Cytoscape, and hub genes were identified. The promoter sequences of these genes were analyzed using Plantcare. Finally, the expression of COP1 gene was evaluated using Real-time PCR.
 
Results
RNA-seq analysis using de novo assembly-based and reference genome-based methods identified 1602 transcripts and 272 genes with distinct expression patterns. Study on GRN and PPI networks led to the discovery of 29 hub genes, including BAK1, ETR1, GER3, HSP70, CDKB2;2, CAS, GRDP1, BSL3, CPN20, AOR, MCM7, DXS, AdoMet-MTases, RCA, CYP90C1, C3H37, CDPK6, Lac1, WRKY50, COP1, PP2C76, CaM-7, Histone H1-3, PPR, LRR-RLK, LACS, LUT5, and Clp5, which play roles in key cellular processes such as plant hormone regulation (ABA, BR, ethylene), MAPK signaling, RNA processing, photosynthesis, stomatal control, protein structure maintenance, and cell cycle. Promoter analysis revealed the existence of important motifs including W-box, TGA-box, ERE, ABRE, MYC, MYB and MBSI and MBS GT-1 motif which led to the co-regulatory role in salt stress response. The real time PCR results of the COP1 gene, which is one of the ABA-activated genes, were consistent with its expression profile from RNA-seq analysis.
Conclusion
The current study through systems biology approach revealed that sunflower directs gene functions in central biological activities, such as plant hormone signaling pathways (ABA, BR and ethylene), MAPK pathway RNA transport, photosynthesis, stomatal function control protein structure stabilization, the cell cycle etc., under salt stress.These results enhance our understanding of the molecular basis of salinity tolerance and can be used to genetically engineer sunflowers for enhanced salinity resistance.

کلیدواژه‌ها [English]

  • Gene regulatory network (GRN)
  • Promoter analysis
  • Protein-protein interaction network (PPI)
  • Salinity stress
  • Sunflower

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مجله بیوتکنولوژی کشاورزی
دوره 18، شماره 2
خرداد 1405
صفحه 69-114

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