Comparative analysis of whole flower transcriptomes in the Zingiberales

PeerJ
Ana Maria R AlmeidaChelsea D Specht

Abstract

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with...Continue Reading

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

TransDecoder
Blast
Trimmomatic
Blastn
RSEM
HMMER3
Trinity
cutadapt
EVAL
DIVARICATA

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