The Construction of Genome Annotation Database for Liverwort

The liverwort Marchantia polymorpha L. is dioecious and haploid in most of its life cycle. Its phylogenetic position and low genetic redundancy have made M. polymorpha an attractive unique model plant. The genome size of Marchantia 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; female) genome has been sequenced by a group centered upon Kyoto University using Solexa GAII (illumina. Inc.). 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.

We have integrated the genomic data with polymorphisms (approx. 150,000 SNPs and 27,000 indels) between BC4 and Kit2, RNA-Seq and DNA makers to build an annotation database of the Marchantia genome. The annotation database builds on WebApollo (http://www.gmod.org/wiki/WebApollo) of the community annotation platform. Recently we have been adding the functions to the database such as the following: (1) the links between genetic marker information and scaffolds, (2) the genome browsing of respective scaffold, (3) improvement of gene prediction accuracy using RNA-Seq data, (4) semi-automated identification of gene structures.

Thus the database leads to accumulation and sophistication of gene annotation by multiple researchers and promote the use of M. polymorpha as a model plant by research communities.