Fully automated pipeline for detection of sex linked genes using RNA-Seq data

0446325 - BFÚ 2016 RIV GB eng J - Journal Article
Michalovová, Monika - Kubát, Zdeněk - Hobza, Roman - Vyskot, Boris - Kejnovský, Eduard
Fully automated pipeline for detection of sex linked genes using RNA-Seq data.
BMC Bioinformatics. Roč. 16, č. 78 (2015). ISSN 1471-2105. E-ISSN 1471-2105
R&D Projects: GA ČR(CZ) GBP501/12/G090; GA MŠMT(CZ) LM2010005
Institutional support: RVO:68081707
Keywords : SILENE-LATIFOLIA * RUMEX-ACETOSA * Y-CHROMOSOME
Subject RIV: BO - Biophysics; EF - Botanics (UEB-Q)
Impact factor: 2.435, year: 2015

Background: Sex chromosomes present a genomic region which to some extent, differs between the genders of a single species. Reliable high-throughput methods for detection of sex chromosomes specific markers are needed, especially in species where genome information is limited. Next generation sequencing (NGS) opens the door for identification of unique sequences or searching for nucleotide polymorphisms between datasets. A combination of classical genetic segregation analysis along with RNA-Seq data can present an ideal tool to map and identify sex chromosome-specific expressed markers. To address this challenge, we established genetic cross of dioecious plant Rumex acetosa and generated RNA-Seq data from both parental generation and male and female offspring. Results: We present a pipeline for detection of sex linked genes based on nucleotide polymorphism analysis. In our approach, tracking of nucleotide polymorphisms is carried out using a cross of preferably distant populations.
Permanent Link: http://hdl.handle.net/11104/0248351