Abstract:
BACKGROUND : Seagrasses (Alismatales) are the only fully marine
angiosperms. Zostera marina (eelgrass) plays a crucial role in the
functioning of coastal marine ecosystems and global carbon
sequestration. It is the most widely studied seagrass and has become
a marine model system for exploring adaptation under rapid climate
change. The original draft genome (v.1.0) of the seagrass Z. marina
(L.) was based on a combination of Illumina mate-pair libraries
and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger
sequence was obtained representing 47.7× genomic coverage. The
assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final
genome assembly size of 203MB, 20,450 protein coding genes and
63% TE content. Here, we present an upgraded chromosome-scale
genome assembly and compare v.1.0 and the new v.3.1, reconfirming
previous results from Olsen et al. (2016), as well as pointing out new
findings.
METHODS : The same high molecular weight DNA used in the original
sequencing of the Finnish clone was used. A highquality
reference genome was
assembled with the MECAT assembly pipeline combining PacBio longread
sequencing and Hi-C scaffolding.
RESULTS : In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored
scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB,
showing high contiguity and few gaps (~0.5%). 21,483 proteinencoding
genes are annotated in this assembly, of which 20,665
(96.2%) obtained at least one functional assignment based on
similarity to known proteins.
CONCLUSIONS : As an important marine angiosperm, the improved Z.
marina genome assembly will further assist evolutionary,
ecological, and comparative genomics at the chromosome
level. The new genome assembly will further our understanding into
the structural and physiological adaptations from land to marine life.
