سرهم‌بندی نوپدید ترنسکریپتوم و شناسایی ریز RNAهای محافظت‌شدة Kelussia odoratissima Mozaff.

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی دکترا، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرم‌آباد، ایران

2 استاد، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرم‌آباد، ایران

3 دکتری تخصصی، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرم‌آباد

چکیده

گیاه دارویی کلوس یا کرفس‌کوهی (Kelussia odoratissima Mozaff.) منبعی غنی از مواد فعال دارویی با اثرات درمانی است که به‌صورت انحصاری در رشته‌کوه‌های زاگرس مرکزی ایران یافت می‌شود. با وجود خطر انقراض این‌گونه گیاهی، اطلاعاتی درباره ژنوم / ترنسکریپتوم و بیوسنتز ترکیبات ارزشمند این گیاه وجود ندارد. در بین مولکول‌های حیاتی، اگرچه مولکول‌های microRNA (miRNAs) نقش مهمی در فرآیندهای مختلف زیستی به‌ویژه در بیوسنتز متابولیت‌های ثانویه در گیاهان دارویی دارند، در حال حاضر، هیچ گزارشی از وضعیت miRNAها در گیاه کلوس منتشر نشده است. مطالعه حاضر به‌منظور شناسایی miRNAهای محافظت‌شده و ژن‌های هدف آن‌ها در ترنسکریپتوم برگ کلوس انجام شد. پس از توالی‌یابی RNA با پلتفرم Illumina HiSeq 2500، خوانش‌های کوتاه پردازش شده سرهم‌بندی شدند. در این مطالعه، تعداد 4658 یونی‌ژن حاوی توالی miRNAهای بالقوه شناسایی شدند. پس از پالایه کردن دقیق، پنج توالی miRNA (miR156-3P، miR408، miR169، miR171 و miR398) از میان توالی‌های نامزد شناسایی و ژن‌های هدف آن‌ها مشخص شدند. نتایج این مطالعه نشان داد که miRNAها در مسیرهای متابولیکی مختلفی از جمله متابولیسم بوتانوات، متابولیسم گلیکوزیلات و دی‌کربوکسیلات، متابولیسم نشاسته و ساکارز، تثبیت کربن در اندامک‌های فتوسنتزی، تخریب پراکسی‌زوم و تخریب اسیدهای چرب درگیر بودند. miR408 با تنظیم ژن‌های شش مسیر متابولیکی، به‌عنوان تأثیرگذارترین miRNA محافظت‌شده در پروفایل بیانی کلوس شناخته شد. به‌طور کلی، با توجه به نقش تنظیمی miRNAهای شناسایی‌شده بر روی طیف گسترده‌ای از شبکه‌های ژنی و فرآیندهای بیولوژیکی گیاه کلوس در مطالعه حاضر، می‌توان از این miRNAها به‌عنوان ژن‌های نامزد برای بهبود صفات کمی و کیفی این گیاه استفاده‌کرد.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

De novo transcriptome assembly and conserved microRNAs identification of medicinal plant, Kelussia odoratissima Mozaff.

نویسندگان [English]

  • Maryam Ramezani 1
  • Farhad Nazarian-Firouzabadi 2
  • Ahmad Ismaili 2
  • Seyed Sajad Sohrabi 3
1 Ph.D. Student, Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
2 Prof., Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
3 Ph.D., Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
چکیده [English]

Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds biosynthesis pathways. MicroRNAs (miRNAs) play an important role in different processes such as growth and development, cell proliferation, response to stresses and biosynthesis metabolite. As far as the bioinformatic data are concern, the genome/transcriptome of kelus has not been sequenced. The present study was performed to identify the conserved miRNAs and their target genes in the kelus leaf transcriptome. After pair-end sequencing with the Illumina HiSeq 2500 platform, clean reads were assembled. In total, 4658 unigenes were found to contain potential miRNAs sequences. Following strict filtering criteria, five miRNAs belonging to five conserved miRNA families (miR156-3P, miR408, miR169, miR171 and miR398) were identified among candidate sequences. Results of this study revealed that the target genes of the identified miRNAs were involved in various metabolic pathways, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, peroxisome degradation, and fatty acid degradation. By affecting genes associated with six metabolic pathways, miR408 was identified as the most influential conserved microRNA in the kelus leaf transcriptome. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of kelus, these miRNAs can be used as candidate genes for breeding kelus quantitative and qualitative traits.

کلیدواژه‌ها [English]

  • Gene network
  • Kelus
  • miR408
  • Secondary metabolites
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