Lytechinus variegatus

About L.variegatus

Lytechinus variegatus Lamarck, 1816 is known as the green sea urchin or variegated sea urchin. It has many color morphs including white, green, purple, red, or pink or a combination of those colors. There are multiple subspecies for this species and the distribution details are in flux.


The animals used for sequencing and generally used for experimental work come from the coast of North Carolina and Florida. Lytechinus variegatus is an often-used model that shared a common ancestor with the purple sea urchin about 50 MY ago. Besides gene discovery another important use of the Lv genome sequence is comparative genomics, to identify and characterize cis regulatory modules. Unless they are functional, non-coding sequences will have changed from those of the common ancestor through genetic drift over this divergence time. Many fragments were identified in this manner and a majority of the active cis-regulatory modules (CRM) for a gene under study will be found in the patches of conserved sequences identified by an un-gapped comparison using a sliding window technique.

The L. variegatus draft genome sequence was assembled from about 13X Roche 454 reads determined from fragment and 2.5 Kb insert paired ends and approximately 21X Illumina reads. This data set (version 0.4) was submitted to NCBI on December 22, 2011 (Accession GCA_000239495.1). The genome assembly is 835 Mb in length with a contig N50 size of 6.05kb and scaffolds N50 size of 39.17 kb. The latest version of the Lv genome (v2.2) is an upgrade of version 0.4 using PacBio reads with an N50 length of 2.9kb which produced an improved assembly with a contig N50 of 9.7 kb and a scaffold N50 of 46 Kb.

Sequence and Scaffold statistics

Assembly Type Number N50(kb) Bases+Gaps(Mb) Bases(Mb)
Lvar_v2.2 Scaffolds 322,794 46.2 1,061 1,004
Lvar_v2.2 Contigs 452,418 9.6 1,004, 1,004