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

Kiruba S Arun-Chinnappa,David W Mccurdy

doi:10.3389/fpls.2015.00217

Kiruba S Arun-Chinnappa, David W Mccurdy

Open Access

https://doi.org/10.3389/fpls.2015.00217

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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.

Highlights

The introduction of RNA sequencing (RNA-Seq) has widened the use of plant species for molecular genetic analyses beyond those for which full genome sequences are available
To provide a platform for future RNA-Seq analysis of gene expression during transfer cell (TC) differentiation, in this communication we report the de novo assembly of a genome-wide transcriptome map of V. faba using Illumina-based 100 bp paired-end sequencing
We have generated a genome-wide transcriptome map of V. faba to provide a reference for future RNA-Seq-based transcript profiling of TC development

Summary

Introduction

The introduction of RNA sequencing (RNA-Seq) has widened the use of plant species for molecular genetic analyses beyond those for which full genome sequences are available. In addition to its importance as a crop species worldwide, V. faba is widely used in plant physiology research to study such processes as guard cell dynamics in leaves (Fukuda et al, 1998; Fellè et al, 2000), transport processes in phloem (Thorpe et al, 2010; Hafke et al, 2013), and importantly for this study, transfer cell (TC) development in cotyledons (Offler et al, 2003) In the latter case, when isolated cotyledons are placed in culture, adaxial epidermal cells trans-differentiate to become functional epidermal TCs (Farley et al, 2000; Dibley et al, 2009). This study estimated that TC formation in this system may involve differential expression of approximately 650 different genes (Dibley et al, 2009), a total approaching the minimum 815 genes determined from a 12 K microarray analysis to be differentially expressed during nucellar projection and endosperm TC development in barley grains (Thiel et al, 2008)

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