Abstract Detail

Genomics / Proteomics

Peredo, Elena L [1], Cardon, Zoe [1], Thomas, Suzanne [1], Bruce, Douglas [2].

De novo transcriptome assembly and gene expression profiling of the desiccation-tolerant desert green alga Scenedesmus rotundus during desiccation and rehydration.

Colonization of land was key for the radiation of life on Earth, and among green plants, embryophytes have long been studied in an effort to identify traits essential for the terrestrial photosynthetic lifestyle. Traits shared among terrestrial embryophytes may be shared because they are important for terrestriality, or they may be shared simply because they were present in the common ancestor of the embryophytes. To tease apart these two possibilities, we are studying multiple lineages of green algae that independently made a permanent leap from water to land. These diverse green algae inhabit biological soil crusts (microbiotic crusts) of the Southwestern U.S. deserts. Desert algae display a very powerful mechanism protecting the photosynthetic apparatus during desiccation and rehydration. Under common garden conditions, desiccation-tolerant species regain photosynthetic activity almost immediately upon rehydration after full desiccation, much more readily than their close aquatic relatives. Slow desiccation leads to stronger photoprotection, suggesting that time is required for these desert algae to fully activate the mechanisms that promote a dissipative state. To investigate the molecular basis of the photoprotective mechanisms triggered during slow desiccation (over 12 hours), we characterized nuclear and organellar gene expression profiles over a time course of slow desiccation and fast rehydration in the desert alga Scenedesmus rotundus (isolated from the Sevilleta LTER, NM). To avoid biasing against recovery of chloroplast and mitochondrial transcripts, we avoided commonly-used Poly(A)-based methods of removing the ribosomal RNA (rRNA) that would otherwise swamp our sequencing effort. Instead, we generated paired-end strand-specific cDNA libraries and used sequence-based, customized, enzymatic targeted removal of S. rotundus rRNA (InDA-C, Nugen) during library preparation. rRNA can constitute up to 90% of total RNA, so such a depletion step is required to ensure sufficient sequencing of mRNA. Illumina NextSeq sequencing of ten libraries (five time points, two biological replicates) generated ~200 million reads, used for de novo assembly of a reference transcriptome for the species (Trinity). Contig annotation and gene ontology were performed using SwissProt and NCBI nr databases (Trinotate and Blast2go). Differential expression analysis was completed according to the Trinity pipeline (RSEM/Bowtie2/DESeq2). We did not find drastic expression changes in early stages of desiccation (0 – 2.5 hours), however, up- and down-regulation of genes became clear by 7.5 hours, and strong upregulation of hundreds of genes was observed in dry samples. Desiccation-associated expression changes were persistent one hour after rehydration.

1 - Marine Biological Laboratory, The Ecosystems Center, 7 MBL St, Woods Hole, MA, 02543-1015, USA
2 - Brock University, Department of Biological Sciences, 500 Glenridge Ave, St. Catharines, ON, ON L2S 3A1

Keywords:
desiccation tolerance
Transcriptomics
green algae
land colonization
photoprotection.

Presentation Type: Oral Paper
Session: 19, Genomics & Proteomics I
Location: 105/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 8:45 AM
Number: 19004
Abstract ID:375
Candidate for Awards:Margaret Menzel Award