Abstract Detail

Genomics / Proteomics

Barrett, Craig [1], Perez, Leticia [2].

Gene expression and mycoheterotrophy: an exploratory analysis of green vs. non-green Corallorhiza (Orchidaceae).

Studies of genome evolution in parasitic and mycoheterotrophic plants have focused overwhelmingly on changes occurring in the plastid genome (plastome) as a result of relaxed selection on photosynthetic function. Only a handful of studies have focused on the effects of photosynthetic loss and patterns of gene expression. While studies have addressed gene expression patterns between holoparasites and their host plants, almost no data exist on expression related to obligate interactions between mycoheterotrophs (viz. holomycotrophs) and their fungal hosts. Here we examine the orchid genus Corallorhiza to compare gene expression patterns across green, partially mycoheterotrophic species vs. non-green, holomycotrophic species. Specifically, we address hypotheses concerned with loss of photosynthesis in holomycotrophs, and changes in expression patterns between orchids parasitizing different hosts. Green species (C. trifida, C. wisteriana) are hypothesized to express photosynthesis-related genes (nuclear and plastid) at some level in contrast to non-green species (C. striata var. striata, C. maculata var. occidentalis). A single representative of each of the aforementioned species was collected at a site where they are sympatric in Montana, USA, all at the same time of day and at the same developmental stage (pre-anthesis). Material was chopped finely in the field and stored immediately in cold RNA-later solution to preserve mRNA. Total RNAs were extracted from whole shoots and rhizomes after cleaning with nuclease free water using the Zymo Plant RNA kit, which has a DNA-exclusion step, followed by treatment with DNAse. Total mRNAs were sequenced after rRNA exclusion and poly-A purification on an Illumina NextSeq500 for 150 bp paired-end reads. Shoot-derived reads were assembled de novo into contigs using Trinity after digital normalization. Plastid contigs were mapped to previously sequenced plastomes of Corallorhiza and annotated, while nuclear contigs were annotated based on the recently published Phalaenopsis genome. Photosynthesis related unigenes were scored as present or absent, and compared qualitatively between green vs. non-green species, as acquisition of biological replicates within species was not yet possible. Unigenes missing from both non-green orchid datasets but present in both green orchid datasets were considered putative gene losses, pseudogenes, or extreme instances of down-regulation. Reads from rhizome mRNAs were mapped simultaneously to recently sequenced orchid and fungal genomes (fungal families Russulaceae or Thelephoraceae), followed by de novo assembly. Differences in transcript presence/absence is discussed, as are future efforts to collect biological replicates and other taxa in Corallorhiza and leafy relatives, with the goal of a phylo-comparative assessment of gene expression.

1 - West Virginia University, Plant and Soil Sciences, G153 South Agricultural Sciences Building, Morgantown, WV, 26506, USA
2 - California State University, Los Angeles, Biological Sciences, 5151 State University Drive, Los Angeles, CA, 90032, USA

Keywords:
Transcriptome
mycoheterotroph
orchid
photosynthesis
parasite
RNAseq
gene expression.

Presentation Type: Poster
Session: P, Genomics/Proteomics Posters
Location: Exhibit Hall/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 5:30 PM This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PGP004
Abstract ID:242
Candidate for Awards:None