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. 2023 Mar 16;114(1):81-87.
doi: 10.1093/jhered/esac056.

A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi

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 draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi

Shannon Rose Kieran Blair et al. J Hered. .

Abstract

We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome's 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development.

Keywords: Anostraca; CCGP; California Conservation Genomics Project; branchiopods; conservation genomics; crustaceans.

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Figures

Fig. 1.
Fig. 1.
(A) A microscope image of Branchinecta lynchi females at 10×. (B) A large vernal pool being dip-net in Solano County, CA. Photos courtesy Shannon Kieran Blair.
Fig. 2.
Fig. 2.
(A) K-mer spectra produced by genoscope. (B) BlobToolKit snail plot showing N50 metrics for Branchinecta lynchi assembly and BUSCO scores for the Arthopoda set of orthologs. (C) Contact map of the final assembly. This map visualizes the high percentage of sequence contained in scaffolds, suggesting high contiguity of the assembly.
Fig. 3.
Fig. 3.
Male/female coverage ratio of each of the 22 chromosome-length scaffolds for the B. lynchi assembly. No scaffold had high enough coverage differential to be considered a likely sex chromosome. Genome-wide median coverage ratio was 1.45.
See this image and copyright information in PMC

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