Tigriopus californicus (Copepod, San Diego) Assembly and Gene Annotation

About Tigriopus californicus

T. californicus is a harpacticoid copepod that shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation [1].

Picture credit: Greg Rouse (image source: The Burton Lab site, Scripps Institution of Oceanography, UCSD Marine Biology Research Division)

Assembly

The Tigriopus californicus Illumina sequencing was done by Cofactor Genomics, proximity ligation libraries based on the Chicago and Hi-C methods were prepared by Dovetail Genomics as described previously, PacBio sequencing was performed by the University of North Carolina High Throughput Genomic Sequencing Facility. The resulting Tcal_SD_v2.1 assembly was built and submitted by the Scripps Institution of Oceanography, UCSD Marine Biology Research Division[1].

Annotation

The gene models were predicted [1] at Scripps Institution of Oceanography, UCSD Marine Biology Research Division using MAKER2 pipeline and deposited at GeneBank from where Ensembl Genomes imported the data. Non-coding RNA genes were added using the Ensembl Genomes pipeline.

References

1. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus.
   Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. 2018. Nat Ecol Evol. Vol. 2, Issue 8. doi: 10.1038/s41559-018-0588-1.

Picture credit: Greg Rouse (image source: The Burton Lab site, Scripps Institution of Oceanography, UCSD Marine Biology Research Division)