مقایسه عملکرد ابزارهای سرهم‌بندی ترنسکریپتوم در گیاه زعفران زراعی (.Crocus sativus L)

نوع مقاله : مقاله علمی پژوهشی

نویسندگان

1 دانشجوی دکتری، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج.

2 استادیار پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج.

3 دانشیار پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج.

4 استادیار، پژوهشکده گیاهان و مواد اولیه دارویی، دانشگاه شهید بهشتی، تهران.

10.22048/jsat.2017.87859.1235

چکیده

زعفران گیاه دارویی و ادویه‌ای ارزشمند متعلق به خانواده زنبق و به‌عنوان منبع غنی از آپوکاروتنوئیدها در جهان محسوب می‌شود. به دلیل سایز بزرگ و پیچیدگی ژنوم زعفران توالی‌یابی آن به‌عنوان چالش مطرح است. با ظهور تکنیک‌های توالی‌یابی نسل بعد، توالی‌یابی RNA به‌عنوان منبع غنی مطالعات بیولوژیکی توسعه یافته ‌است. سرهم‌بندی ترنسکریپتوم­ها­ از تعداد بی‌شمار خوانش‌های کوتاه منبعی غنی برای مطالعه گونه‌هایی که ژنوم مرجع آن‌ها در دسترس نیست فراهم می‌کند. اما سرهم‌بندی قرائت­ها و رسیدن به نتیجه مطلوب به‌ویژه برای گیاهان پلی­پلوئید همواره یک چالش بزرگ محسوب می‌شود. در این مطالعه کارایی ابزارهای مختلف سرهم‌بندی با توجه به فاکتورهایی هم­چون طول N50، تعداد کل یونی­ژن‌ها و درصد هم‌ردیفی مورد مقایسه قرار گرفتند. نتایج نشان داد که Bridger به‌عنوان ابزاری بهتر جهت سرهم‌بندی قرائت­های ترنسکریپتوم زعفران است که می­تواند سرهم­بندی بر اساس پارامترهای تعداد ترنسکریپت­ها، طول N50، اندازه کل سرهم­بندی و درصد هم‌ردیفی قرائت­ها به ترنسکریپتوم فراهم آورد. Velvet/Oases بالاترین درصد درهم­ریختگی را نشان می­دهد که منجر می­شود اعضای مختلف یک خانواده ژنی که شباهت بالایی به یکدیگر دارند در یک ترنسکریپت سرهم­بندی شوند. نتایج حاصل از این تحقیق می‌تواند به محققان در جهت انتخاب بهتر ابزار سرهم‌بندی و توسعه ابزارهای موجود راهکارهایی را ارائه نماید.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Comparative performance of transcriptome assembly programs for saffron (Crocus sativus L.)

نویسندگان [English]

  • Maryam Vahedi 1
  • Seyed Alireza Salami 2
  • Majid Shokrpour 3
  • Hassan Rezadoost 4
1 PhD. Student, College of Agriculture and Natural resources, University of Tehran, Karaj, Iran.
2 Assistant professor, College of Agriculture and Natural resources, University of Tehran, Karaj, Iran
3 Associate professor, College of Agriculture and Natural resources, University of Tehran, Karaj, Iran.
4 Assistant professor, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, Tehran, Iran
چکیده [English]

Saffron (Crocus sativus L.) belonging to Iridaceae family as a source of apocarotenoids is one of the most valuable spices and medicinal plants in the world. Because of the large size and high complexity of saffron genome, its sequencing remains a challenge. The arrival of next-generation sequencing technologies (NGS) has allowed the rapid and efficient development for RNA sequencing. De novo assembly of transcriptome from short-read RNA-Seq data provides a great resource for the study of species without a reference genome. De novo assembly of the transcriptome has some unique challenges, particularly in the case of plants, which possess a large amount of paralogs, orthologs, homoeologs and isoforms. In this research, we attempted to compare the performance of de novo assembly tools including BinPacker, Bridger, Oases-Velvet and Trinity through consideration of a quality metrics such as N50 length, the total number of contigs and alignment scores. The results of these analyses revealed that assembly using Bridger had a superior performance for saffron transcriptome, Oases suffered from relatively high chimera rates and redundancies which causes genes family with high similarity assembled into one transcript, Trinity performs worse than Bridger in the increase of false positives. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers.

کلیدواژه‌ها [English]

  • Saffron
  • Assembly
  • BinPacker
  • Bridger
  • Trinity
  • Velvet/Oases
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