Draft genome of tule elk Cervus elaphus nannodes.

Jessica E Mizzi,C Titus Brown,Benjamin N Sacks,Zachary T Lounsberry

doi:10.12688/f1000research.12636.1

Jessica E Mizzi, C Titus Brown + Show 2 more

Open Access

https://doi.org/10.12688/f1000research.12636.1

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Journal: F1000Research	Publication Date: Sep 15, 2017
Citations: 6	License type: CC BY 4.0

Affiliation: University of California, Davis

Abstract

This paper presents the first draft genome of the tule elk ( Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s. The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids.

Highlights

To date, the closest genomic resource for elk (Cervus elaphus) is a full mitochondrial assembly of white-tailed deer (Odocoileus virginianus), a distantly related cervid[1]
Our motivation for generating a genomic resource for the tule elk was to create a reference for identifying single nucleotide polymorphisms (SNPs) to develop assays to monitor elk population abundance and for related population genetic applications
Due to the relatively low coverage generated in this work (40X overall with an average of 10X coverage from each individual), we used the MEGAHIT metagenome assembler, which has been found to perform well on low-quality or low-coverage DNA sequencing in bacteria[5]

Summary

Introduction

The closest genomic resource for elk (Cervus elaphus) is a full mitochondrial assembly of white-tailed deer (Odocoileus virginianus), a distantly related cervid[1]. The present paper presents the first de novo genomic draft of the tule elk (C. elaphus nannodes). This California-endemic elk subspecies underwent a major genetic bottleneck when its numbers were reduced to as few as three individuals in the 1870s2,3. Their numbers have increased to >5,000 today[4], the historical bottleneck left its mark on the elk’s genome, rendering it more homozygous than other elk subspecies. Due to the relatively low coverage generated in this work (40X overall with an average of 10X coverage from each individual), we used the MEGAHIT metagenome assembler, which has been found to perform well on low-quality or low-coverage DNA sequencing in bacteria[5]

Methods

Results

Andrews S