Liverwort Genome Analysis Using DDBJ Pipeline and Construction of the Database Annotated By the Research Communities

The liverwort Marchantia polymorpha L. is dioecious and haploid in most of its life cycle. Its phylogenetic position, low genetic redundancy and available molecular genetic resources have made M. polymorpha an attractive unique model plant. The Marchantia genome is composed of eight chromosomes and a sex chromosome, X or Y, and its genome size is estimated to be 280 Mb. The genome of BC4, a line established by backcrossing the M. polymorpha accession Takaragaike1 (Tak1; male) to the accession Takaragaike2 (Tak2; female), has been draft-sequenced by DOE Joint Genome Institute.

The accession Kitashirakawa2 (Kit2; femal) genome has been sequenced by a group centered upon Kyoto University using Solexa GAII (illumina. Inc.). Total 27 Gb of the Kit2 sequence reads were mapped to the BC4 genome, and differences between the two genomes were detected using DDBJ Read Annotation Pipeline (DDBJ Pipeline; http://p.ddbj.nig.ac.jp) developed by Genome Informatics Laboratory of National Institute of Genetics [1]. As the result, approx. 150,000 SNPs and 27,000 indels were detected between the two genomes.

We have integrated the genomic data with those SNPs/indels, RNA-Seq and DNA makers to build an annotation database of the Marchantia genome. The annotation database builds on WebApollo [2] of the community annotation platform, which should lead to accumulation and sophistication of gene annotation by multiple researchers and promote the use of M. polymorphaas a model plant by research communities.

[1] Nagasaki et al. DNA Res. 2013, 20(4):383-90.

[2] Lee et al. Genome Biology 2013, 14:R93.