Marchantia genome

 

Phytozome

The genome of M. polymorpha Tak-1 strain has been sequenced and made available as an early release through Phytozome (Goodstein et al. 2012) by the M. polymorpha community sequencing effort. There are about 20,000 loci in Marchantia genome.

Screen Shot 2017-07-10 at 13.41.10.png

MarpoDB

Constructed by Bernardo Pollak and Mihails Delmans in Jim Haseloff Lab, MarpoDB (Delmans et al, 2017) is a gene-centric database for Marchantia polymorpha Cam-1 strain genetic parts designed for genetic engineering and synthetic biology purposes. In version 3 of MarpoDB there are about 13,000 loci identified. You can BLAST to MarpoDB and HMMER to MarpoDB, and you can now search the database with Phytozome ID (ticking "DBxref" button).

For each gene you'll find the genomic sequence of the genes, 5UTR-CDS-3UTR with exons and intons, as well as 3kb upstream and downstream for promoter elements and terminator sequences. Exporting sequence with annotations is very easy, just click the "genebank file" button at the bottom, making it easy to use the database to extract DNA parts for modular and standardised DNA assembly.

Nomenclature

The paper by Bowman et al. “The Naming of Names: Guidelines for Gene Nomenclature in Marchantia.” (2016), outlines community guidelines for M. polymorpha gene and transgene nomenclature, to promote consistency and reduce both redundancy and confusion in the scientific literature.

More details in Marchantia nomenclature