Comparative analysis of tandem repeats in four Aubrieta genomes

Document Type : Research Paper

Authors

1 Department of Plant Protection, Faculty of Agriculture, University of Kufa Najaf-Iraq

2 University of Duhok College of Agricultural Engineering Sciences Kurdistan Region of Iraq Duhok

3 , Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom & Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China

10.22092/ijb.2024.364281.1443

Abstract

The genus Aubrieta Adan. (Brassicaceae) is widely distributed and diverged across different elevations. The genome components and organization of this plant are still less understood. Tandemly repeated sequences were examined in whole genome raw reads of four Aubrieta species using Next Generation Sequencing (NGS) and bioinformatics techniques. Six clusters of tandem repeats were found based on RepeatExplorer and TAREAN pipelines; one cluster in A. pinardii (ApinSAT1L) and A. scardica (AscaSAT95 H), two clusters in A. erubescens (AeurSAT132L and AeurSAT230L), and A. gracilis (AgraSAT2L and AgraSAT15H) with the GenBank accession numbers (PP391544, PP391547, PP391548, PP391549, PP391545, PP391546) respectively, have been found within all examined genomes. The tandem repeated features were confirmed using de novo assembly contigs. Variable numbers of genome proportions and copies have been recorded for these elements. Aubrieta erubescens has a high copy number compared to A. scardica which has lower copies. The arrangement of tandem repeat clusters within the genome was tandemly organized except for A. scardica (AscaSAT95 H) which was dispersed. Therefore, these genomes can be explained in terms of composition, structure, and evolutionary relationships.

Keywords

Article Title [Persian]

تجزیه و تحلیل مقایسه‌ای توالی‌های تکرار شده در ژنوم چهار گونه از جنس Aubrieta (Brassicaceae)

Authors [Persian]

  • اسامة ناظم العیساوی 1
  • جوتیار محمد 2
  • پاتریک هسلوپ هاریسون 3
1 گروه آموزشی حفاظت گیاهی، دانشکده کشاورزی، دانشگاه کوفه، نجف، عراق
2 دانشکده علوم مهندسی کشاورزی، دانشگاه دهوک، منطقه کردستان عراق
3 گروه آموزشی ژنتیک و بیولوژی ژنوم، موسسه آینده محیط زیست، دانشگاه لیستر، انگلستان و آزمایشگاه‌های حفاظت منابع گیاهی و مصرف پایدار، استان گوانگدونگ چین و باغ گیاه‌شناسی جنوب چین، آکادمی علوم گوانگژو، چین
Abstract [Persian]

گونه‌های جنس Aubrieta Adan. (Brassicaceae) به‌طور گسترده در ارتفاعات مختلف پراکنده و از یکدیگر جدا شده‌اند. اجزا و سازمان ژنوم این گیاهان هنوز کمتر شناخته شده است. توالی‌های تکرار شده پشت سر هم در قرائت‌های خام کل ژنوم چهار گونه Aubrieta با استفاده از روش‌های توالی‌یابی نسل بعدی (NGS) و بیوانفورماتیک مورد بررسی قرار گرفتند. با استفاده از نرم افزارهای RepeatExplorer و TAREAN شش دسته توالی‌های تکراری بدست آمدند. یک دسته در A. pinardii (ApinSAT1L) ویک دسته در A. scardica (AscaSAT95 H) و دو دسته در A. erubescens (AeurSAT132L and AeurSAT230L) و دو دسته در A. gracilis (AgraSAT2L and AgraSAT15H)، به ترتیب با شماره ردیف های بانک ژنPP391544, PP391547, PP391548  PP391549, PP391545, PP391546, در همه ژنوم‌های بررسی شده مشاهده گردید. ویژگی‌های تکرارهای پشت سرهم توالی‌ها با استفاده از روش مونتاژ از نو بخش‌هایی از توالی‌های DNA که به‌گونه‌ای همپوشانی دارند، تأیید شدند. تعداد متغیری از نسبت‌ها و کپی‌های ژنوم برای این عناصر ثبت شده است. Aubrieta erubescens در مقایسه با A. scardica که کپی‌های کمتری دارد، تعداد کپی بالایی دارد. ترتیب خوشه‌های تکرار پشت سر هم در ژنوم به جز A. scardica (AscaSAT95 H) که پراکنده شده بود به‌صورت پشت سر هم سازماندهی شد. بنابراین، این ژنوم‌ها را می‌توان از نظر ترکیب، ساختار و روابط تکاملی توضیح داد. تعداد متغیری از نسبت‌ها و کپی‌های ژنوم برای این عناصر ثبت شده است. Aubrieta erubescens در مقایسه با A. scardica که کپی‌های کمتری دارد، تعداد کپی بالایی دارد. ترتیب خوشه‌های توالی‌های تکراری پشت سر هم در ژنوم به‌جز A. scardica (AscaSAT95 H) که پراکنده شده بود، به‌صورت پشت سر هم سازماندهی شد. بنابراین، این ژنوم‌ها را می‌توان از نظر ترکیب، ساختار و روابط تکاملی توضیح داد.

Keywords [Persian]

  • Brassicaceae
  • evolution
  • repeat sequences
  • next-generation sequencing (NGS)
  • bioinformatics

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History

  • Receive Date: 02 December 2023
  • Revise Date: 27 February 2024
  • Accept Date: 08 April 2024

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