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 forexploringadaptation 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 andfosmid-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 486Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here,we present an upgraded chromosome-scale genome assemblyand comparev.1.0and the newv.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods:The same high molecular weight DNAused in the original sequencingof the Finnish clonewas used.Ahigh-qualityreferencegenome was assembledwiththeMECATassemblypipelinecombiningPacBiolong-readsequencingand Hi-C scaffolding. Results:In total,75.97 GbPacBiodata wasproduced.The final assembly comprisessixpseudo-chromosomesand304 unanchored scaffolds with a total length of 260.5Mb andanN50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding 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:Asanimportant marine angiosperm,the improved Z. marinagenomeassemblywillfurtherassistevolutionary, ecological,and comparative genomicsat the chromosome level.Thenew genome assemblywillfurther our understandinginto the structural and physiological adaptations from land to marinelife.
Highlights
Seagrasses are a polyphyletic assemblage of early-diverging monocotyledoneous plants belonging to the Alismatales (Les, Cleland, and Waycott 1997; Du and Wang 2016); they are not true grasses (Poaceae)
We identified noncoding RNAs, such as microRNAs, small nuclear RNAs and ribosomal RNAs by comparing with known noncoding RNA libraries (Rfam v14.2), using the cmscan program of Infernal v1.1.2 (Nawrocki and Eddy 2013)
Genome size and assembly A single genotype of Z. marina from the northern Baltic Sea, Finnish Archipelago Sea had been subjected to whole-genome assembly using Sanger and Illumina sequencing (Olsen et al 2016)
Summary
Seagrasses are a polyphyletic assemblage of early-diverging monocotyledoneous plants belonging to the Alismatales (Les, Cleland, and Waycott 1997; Du and Wang 2016); they are not true grasses (Poaceae). Several clades of seagrasses arose independently from freshwater sister taxa 3-4 times between the Paleocene and late Eocene (~65-34 mya) and are the only fully marine, flowering plants (~14 genera and ~65 species) (Chase et al 2016) They occur in predominantly soft-sediment, marine coastal environments worldwide (Green, Short, and Frederick 2003) and as engineering species provide the foundation of three-dimensional habitats that are among the most productive and biodiverse (Costanza et al 1997; Duffy et al 2015). Seagrass meadows provide numerous ecosystem services, e.g., provisioning of fish and invertebrates, retention of nutrients (Larkum, Orth, and Duarte 2006) and carbon sequestration (Fourqurean et al 2012) They are under threat related to human impacts (Waycott et al 2009) that fundamentally change coastal system dynamics (Duffy et al 2015) and make restoration extremely difficult (van Katwijk et al 2016).
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
