Title: Transcriptional correlates of sexual/asexual life history traits in Marchantia

RNA-seq (massively parallel RNA sequencing) will be used to characterize the genes that are expressed in developing sexual and asexual reproductive structures in the basal plant Marchantia. Raw data consisting of ~500 million short nucleotide sequence reads will be assembled de novo and expression of genes and alternatively spliced isoforms will be quantified by mapping reads from each trait state back to the full assembly. The assembly will be screened for similarity against existing genomic databases to assign putative functional annotations in order to assess whether specific types of genes are disproportionately expressed in different portions of the sexual/asexual pathway.

Students:

Hansika Herath (Graduate Student) Added 02/18/2021

Software:

De novo transcriptome assembly - Trinity - Available at UK, but may require run times in excess of 7 days and may consume 100-500 GB RAM

Read mapping - Hisat2 - Stringtie

Sequence similarity searching - NCBI Blast 2.2.28+ - Available at UK

Functional annotation - BLAST2GO - Available at UK, but free version is limited in functionality. Commercially available versions would be helpful if accessible.

Representation analysis - DAVID, PANTHER - Available at UK

The software listed above are all under active development and improvement. Genome and transcriptome assembly, read mapping, and functional annotation represent areas of rapid innovation and other software packages may be utilized as they become available.

Collaborators:

Jessica Brzyski (non-UK collaborator)

Rose Marks