SEQUENCING AND DE NOVO TRANSCRIPTOME ASSEMBLY OF STELLARIA MEDIA (L.) VILLтезисы доклада

Работа с тезисами доклада


[1] Sequencing and de novo transcriptome assembly of stellaria media (l.) vill / M. S. Belenikin, A. S. Speranskaya, N. V. Melnikova et al. // VIII International Conference on Bioinformatics of Genome Regulation and StructureBiology (BGRS-2012)/ International Conference on Postgenomic Technology for Biomedicine (PTB-2012). — Novosibirsk, 2012. 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.

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