De Novo Assembly of the Transcriptome of the Non-Model Plant Streptocarpus rexii Employing a Novel Heuristic to Recover Locus-Specific Transcript Clusters

Matteo Chiara,Alberto Spada,David S. Horner

doi:10.1371/journal.pone.0080961

Abstract

De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database.

Highlights

The molecular mechanisms that underlie the generation and diversification of evolutionary novelties is one of the key issues in developmental biology [1]
Continued growth of these structures is orchestrated from a nexus of three meristems at the junction of the lamina and petiolode: (a) the basal meristem which provides the growth of the lamina; (b) the petiolode meristem, involved in the growth of the midrib and elongation of the petiolode; (c) the groove meristem which provides the growth of new phyllomorphs and inflorescences
We provide simple metrics to evaluate the impact of the method when a reference genome is not available and apply the clustering strategy to transcripts reconstructed from a novel high throughput RNA sequencing dataset from S. rexii

Summary

Introduction

The molecular mechanisms that underlie the generation and diversification of evolutionary novelties is one of the key issues in developmental biology [1] In this respect, the genus Streptocarpus Lindl, which includes caulescent species that produce leaves from a conventional shoot apical meristem (SAM) as well as acaulescent species - both unifoliate (possessing only a single leaf throughout the individual’s life), and rosulate such as Streptocarpus rexii (producing several leaves arranged in a more or less irregular rosette) - is of particular interest. Streptocarpus, and other Old World Gesneriaceae, exhibit anisocotyly, the unequal development of cotyledons after germination whereby the first phyllomorph is derived from the continued growth of one of the two cotyledons to form the macrocotyledon (cotyledonary phyllomorph), from the activity of the basal meristem [3]

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Conclusion