Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development

Abstract

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.

Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions

“…The R . cantleyi transcriptome was sequenced in-house, producing 40,768,187 high quality reads 16 . The consensus contigs of P .…”

“…RNA integrity was assessed using Agilent BioAnalyzer (Agilent Technologies, USA) and the quality was examined using Spectrophotometer ND-1000 (NanoDrop, USA). After cDNA preparation and library construction using TruSeq RNA Sample Prep kit, the sample was sequenced using the Illumina Solexa platform 16 . The raw data was preprocessed and annotated using BLAST v2.2.26 46 , and Blast2GO 48 .…”

“…We report here the results of a comparative survey of nucleus-encoded proteins targeting the plastid using RNA-Seq data obtained from Lee et al . 16 and public databases. We observed that R .…”

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

“…Therefore, to obtain information about the nuclear genes, scientists often sequence the transcriptome instead of the genome itself. Various studies of nuclear genomes, including studies based on the transcriptome analysis, revealed several features characteristic of genomes of non-photosynthetic plants (Wickett et al, 2011; Lee et al, 2016; Schelkunov, Penin & Logacheva, 2018; Yuan et al, 2018). First, just as in the plastid genomes, there is an extensive loss of photosynthesis-related genes.…”

Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development

“…Substantial progress has been achieved in understanding the mechanism of flower development, particularly in Arabidopsis [8, 10]. However, while considerable work has been carried out in recent years on the different aspects of Rafflesia [11–12] including genes potentially involved in the growth and flower development [13–14], our knowledge regarding the molecular mechanism of R . cantleyi floral development is still very limited due to scarce sample availability, challenges during sample collection, lack of suitable material in the wild, undeveloped analytical methodologies, and inadequate molecular resources.…”