De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research

Publication Overview
TitleDe novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research
AuthorsArun-Chinnappa KS, McCurdy DW
TypeJournal Article
Journal NameFrontiers in plant science
Volume6
Year2015
Page(s)217
CitationArun-Chinnappa KS, McCurdy DW. De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. Frontiers in plant science. 2015; 6:217.

Abstract

Vicia faba (L.) is an important cool-season grain legume species used widely in agriculture but also in plant physiology research, particularly as an experimental model to study transfer cell (TC) development. TCs are specialized nutrient transport cells in plants, characterized by invaginated wall ingrowths with amplified plasma membrane surface area enriched with transporter proteins that facilitate nutrient transfer. Many TCs are formed by trans-differentiation from differentiated cells at apoplasmic/symplasmic boundaries in nutrient transport. Adaxial epidermal cells of isolated cotyledons can be induced to form functional TCs, thus providing a valuable experimental system to investigate genetic regulation of TC trans-differentiation. The genome of V. faba is exceedingly large (ca. 13 Gb), however, and limited genomic information is available for this species. To provide a resource for future transcript profiling of epidermal TC differentiation, we have undertaken de novo assembly of a genome-wide transcriptome map for V. faba. Illumina paired-end sequencing of total RNA pooled from different tissues and different stages, including isolated cotyledons induced to form epidermal TCs, generated 69.5 M reads, of which 65.8 M were used for assembly following trimming and quality control. Assembly using a De-Bruijn graph-based approach generated 21,297 contigs, of which 80.6% were successfully annotated against GO terms. The assembly was validated against known V. faba cDNAs held in GenBank, including transcripts previously identified as being specifically expressed in epidermal cells across TC trans-differentiation. This genome-wide transcriptome map therefore provides a valuable tool for future transcript profiling of epidermal TC trans-differentiation, and also enriches the genetic resources available for this important legume crop species.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-eCollection
ISSN1664-462X
pISSN1664-462X
Publication Date2015
Journal AbbreviationFront Plant Sci
DOI10.3389/fpls.2015.00217
Elocation10.3389/fpls.2015.00217
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountrySwitzerland
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DatabaseAccession
PMID: PubMedPMID:25914703