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. 2023 Mar 16;114(1):74-80.
doi: 10.1093/jhered/esac057.

A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli

Shannon Rose Kieran Blair  1 , Andrea Schreier  1 , Merly Escalona  2 , Amanda J Finger  1 , Shannon E K Joslin  3 , Ruta Sahasrabudhe  4 , Mohan P A Marimuthu  4 , Oanh Nguyen  4 , Noravit Chumchim  4 , Emily Reister Morris  5 , Hayley Mangelson  5 , Joshua Hull  6
Affiliations

A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli

Shannon Rose Kieran Blair et al. J Hered. .

Abstract

We present the novel reference genome of the Versatile Fairy Shrimp, Branchinecta lindahli. The Versatile Fairy Shrimp is a freshwater anostracan crustacean found across the western United States from Iowa to Oregon and from Alberta to Baja California. It is an ephemeral pool specialist, living in prairie potholes, irrigation ditches, tire treads, vernal pools, and other temporary freshwater wetlands. Anostracan fairy shrimp are facing global declines with 3 species in California on the Endangered Species list. This species was included in the California Conservation Genomics Project to provide an easily accessible reference genome, and to provide whole-genome resources for a generalist species, which may lead to new insights into Anostracan resiliency in the face of climate change. The final gapped genome comprises 15 chromosome-length scaffolds covering 98.63% of the 384.8 Mb sequence length, and an additional 55 unscaffolded contigs.

Keywords: Anostraca; CCGP; California Conservation Genomics Project; branchiopoda; crustacean; vernal pool.

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Figures

Fig. 1.
Fig. 1.
(A) A microscope image of Branchinecta lindahli at 10× magnification. (B) A photo of B. lindahli vernal pool habitat in Tulare County, CA. Photos courtesy of Shannon Kieran Blair.
Fig. 2.
Fig. 2.
(A) Kmer spectrum from genomescope. (B) BlobToolKit Snailplot showing N50 metrics for the Branchinecta lindahli assembly and BUSCO scores for the arthropoda set of orthologs. (C) Contact map of assembly. This map shows the high contiguity of this genome, with nearly all (98.6%) sequence contained in the chromosome-level scaffolds.
Fig. 3.
Fig. 3.
Dot-plot of the 15 B. lindahli chromosome-length scaffolds (right) aligned to the B. lynchi genome assembly (top), comprising 22 chromosome-length scaffolds. This dot-plot shows large regions of synteny along with several inversions.
See this image and copyright information in PMC

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