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

Arun-Chinnappa, Kiruba S. and McCurdy, David W. (2015) De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. Frontiers in plant science, 6 (April). pp. 1-9.

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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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Published version made available under open access.
Faculty / Department / School: Current - Faculty of Health, Engineering and Sciences - School of Agricultural, Computational and Environmental Sciences
Date Deposited: 27 Feb 2017 03:07
Last Modified: 20 Mar 2017 06:02
Uncontrolled Keywords: vicia faba; transfer cell research; transfer cell development; transcriptome mapping; genome-wide transcriptome map
Fields of Research : 07 Agricultural and Veterinary Sciences > 0703 Crop and Pasture Production > 070308 Crop and Pasture Protection (Pests, Diseases and Weeds)
Socio-Economic Objective: D Environment > 96 Environment > 9699 Other Environment > 969999 Environment not elsewhere classified
Identification Number or DOI: 10.3389/fpls.2015.00217
URI: http://eprints.usq.edu.au/id/eprint/30668

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