Comparative analysis of whole flower transcriptomes in the Zingiberales

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 special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.

Transcriptome-Wide Analyses Provide Insights into Development of the Hedychium coronarium Flower, Revealing Potential Roles of PTL

“…Analysis of the oral transcriptome of H. coronarium yields insights into its ower development RNA-Seq has become an important tool to unravel the molecular players underlying oral diversi cation in non-model plants that lack a reference genome, such as the Zingiberales. In recent years, whole ower transcriptome libraries of exemplar species from the six families (Musaceae, Lowiaceae, Zingiberaceae, Costaceae, Marantaceae and Cannaceae) comprising the Zingiberales have been generated and analyzed in previous studies [19,30]. Our transcriptome data is consistent in terms of unigene numbers, unigene length distributions, and quality scores with the aforementioned studies.…”

“…The shared oral transcription factors recovered for all species across the exemplar Zingiberales species analyzed, such as LOB40, 41 and 6-like homologs [30], were also identi ed in the H. coronarium oral transcriptome, suggesting that these genes could be conserved regulators of oral development across the Zingiberales. In contrast with previous ndings, a LOB36-like gene which had been formerly recovered only in the banana clade [30], was recovered in our H. coronarium. We also recovered a LOB18-like sequence, which was previously recovered only in the Canna-Calathea lineage (Cannaceae-Marantaceae lineage) and in Zingiber o cinale (Zingiberaceae) [30].…”

“…Comparing our unigenes with previous studies where lineage-speci c genes had been retrieved only in certain lineages within the Zingiberales, some of the most interesting genes were homologs to LOBdomain genes, a plant-speci c transcription factor family which has been implicated in de ning organ boundaries between Arabidopsis ower organs through the negative regulation of brassinosteroid accumulation [23,42], as well as root development, auxin signaling and stress response [43]. The shared oral transcription factors recovered for all species across the exemplar Zingiberales species analyzed, such as LOB40, 41 and 6-like homologs [30], were also identi ed in the H. coronarium oral transcriptome, suggesting that these genes could be conserved regulators of oral development across the Zingiberales. In contrast with previous ndings, a LOB36-like gene which had been formerly recovered only in the banana clade [30], was recovered in our H. coronarium.…”

“…RNA-seq, a cost-effective and highly e cient technology built on small-read sequencing, has accelerated gene discovery across a diverse set of species, while extending our comprehension of complex gene regulatory networks to a wide breath of organisms from the tree of life. In recent years, there has been an explosion in the use of plant transcriptomes as part of a comparative analysis pipeline to isolate homeotic gene orthologs, as well as to study differential gene expression among owers at different developmental stages in a variety of nonmodel species, including some within the Zingiberales [19,[27][28][29][30][31][32]. Here, we conducted de novo transcriptome sequencing of two oral developmental stages for H. coronarium and used comparative transcriptomics combined with Real-time quantitative PCR (qRT-PCR) to investigate gene expression patterns of orthologs of selected ABC-class homeotic genes.…”

Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae)

“…Others have been shown to be repressors or inhibitors of growth ( BB , BPE , BIO , and ELE1 ) or cell division ( DA1/DAR1 ). Even though the prevalence of floral based transcriptomic studies has increased in recent years [ 41 , 42 , 43 , 44 , 45 ], only a limited number of studies have focused on genes associated with flower size differences in non-model taxa including studies in Annona [ 46 ], Chrysanthemum [ 47 ], Lithospermum [ 48 ], Populus [ 49 ], and Saltugilia [ 50 ].…”