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SEQUENCING AND DE NOVO TRANSCRIPTOME ASSEMBLY OF STELLARIA MEDIA (L.) VILLтезисы доклада
- Авторы: Belenikin M.S., Speranskaya A.S., Melnikova N.V., Oparina N.Y., Darii M.V., Dmitriev A.A., Slavokhotova A.A., Korostyleva T.V., Kudryavtseva A.V., Odintsova T.I.
- Сборник: VIII International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2012)/ International Conference on Postgenomic Technology for Biomedicine (PTB-2012)
- Тезисы
- Год издания: 2012
- Место издания: Novosibirsk
- Аннотация: Motivation and Aim: Сommon chickweed Stellaria media (Caryophyllaceae) is cool-season annual weed native to Europe and Russia. This plant is used in traditional medicine and shows effective antiviral activities. It also has a historic traditional human and domestic animals feeding use. Chickweed does not exhibit any symptoms of fungal infection. A number of novel antimicrobial peptides, components of innate immunity were isolated from this plant, that makes it promising object for genetic investigations [1]. Methods and Algorithms: Transcriptome sequencing of 5-old-day seedlings of Stellaria media was performed using next-generation sequencing platform Illumina Genome Analyser and 51х106 of pair-end raw 76 bp sequences were generated. The transcriptomes were assembled using single k-mer assemblers Oases (v.0.2.01) и Trinity (v.2012-03-17). Results: We have performed de novo assembly of obtained paired-end reads using different single k-mer assembly approaches. Oases assembler with 31 k-mer value allowed us to produce ~40,000 transcripts longer than 300 bp. The longest contig was of 5 Kbp length. The total length of assembled transciptome was equal to 22 Mbp. The Oases approach was non effective in graph construction with k-mers values less than 31. Trinity method allows us to produce more than 100,000 transcripts with 9 Kbp length of the longest contig and 112 Mbp of total transcriptome length. Conclusion: We present for the first time the largest dataset of cDNAs (~100000 sequences) for Stellaria media vegetative tissues and also for the total Caryophyllaceae family. The combined usage of two different assemblers proved itself as a reliable strategy. References: 1. A.A.Slavokhotova, T.I.Odintsova, E. A.Rogozhin, A. K.Musolyamov, Y. A.Andreev, E. V.Grishin, T. A. Egorov. Isolation, molecular cloning and antimicrobial activity of novel defensins from common chickweed (Stellaria media L.) seeds. Biochimie. – 2011- V.93.- P. 450 – 456.
- Добавил в систему: Сперанская Анна Сергеевна