Comparative analysis of tandem repeats in four Aubrieta genomes

  • سال انتشار: 1403
  • محل انتشار: مجله گیاه شناسی ایران، دوره: 30، شماره: 1
  • کد COI اختصاصی: JR_IJB-30-1_007
  • زبان مقاله: انگلیسی
  • تعداد مشاهده: 29
دانلود فایل این مقاله

نویسندگان

Osamah Alisawi

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

Jotyar Muhammed

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

Patrick Heslop-Harrison

, 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

چکیده

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 (ApinSAT۱L) and A. scardica (AscaSAT۹۵ H), two clusters in A. erubescens (AeurSAT۱۳۲L and AeurSAT۲۳۰L), and A. gracilis (AgraSAT۲L and AgraSAT۱۵H) with the GenBank accession numbers (PP۳۹۱۵۴۴, PP۳۹۱۵۴۷, PP۳۹۱۵۴۸, PP۳۹۱۵۴۹, PP۳۹۱۵۴۵, PP۳۹۱۵۴۶) 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 (AscaSAT۹۵ H) which was dispersed. Therefore, these genomes can be explained in terms of composition, structure, and evolutionary relationships.

کلیدواژه ها

Brassicaceae, Evolution, repeat sequences, next-generation sequencing (NGS), Bioinformatics

اطلاعات بیشتر در مورد COI

COI مخفف عبارت CIVILICA Object Identifier به معنی شناسه سیویلیکا برای اسناد است. COI کدی است که مطابق محل انتشار، به مقالات کنفرانسها و ژورنالهای داخل کشور به هنگام نمایه سازی بر روی پایگاه استنادی سیویلیکا اختصاص می یابد.

کد COI به مفهوم کد ملی اسناد نمایه شده در سیویلیکا است و کدی یکتا و ثابت است و به همین دلیل همواره قابلیت استناد و پیگیری دارد.