Draft genome of tule elk <i>Cervus canadensis nannodes</i>

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

doi:10.12688/f1000research.12636.2

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Revised

Draft genome of tule elk Cervus canadensis nannodes

[version 2; peer review: 2 approved]

Previously titled: Draft genome of tule elk Cervus elaphus nannodes

Jessica E. Mizzi¹, Zachary T. Lounsberry², C. Titus Brown³, Benjamin N. Sacks ⁴

PUBLISHED 11 Dec 2017

Author details Author details

¹ Microbiology Graduate Group, University of California, Davis, CA, 95616, USA
² Veterinary Genetics Laboratory, University of California, Davis, CA, 95616, USA
³ Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
⁴ Department of Population Health and Reproduction and Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA

Jessica E. Mizzi
Roles: Data Curation, Formal Analysis, Software, Writing – Original Draft Preparation, Writing – Review & Editing

Zachary T. Lounsberry
Roles: Resources, Writing – Review & Editing

C. Titus Brown
Roles: Resources, Supervision, Writing – Review & Editing

Benjamin N. Sacks
Roles: Conceptualization, Funding Acquisition, Resources, Supervision, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

This article is included in the Genomics and Genetics gateway.

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.

Keywords

Cervus elaphus nannodes, genome draft, mammalian genome assembly, tule elk

Corresponding author: Benjamin N. Sacks

Competing interests: No competing interests were disclosed.

Grant information: Support for this project was provided by a grant to BNS from the California Department of Fish and Wildlife, FY1516 Big Game Management Program (Grant ID P1580009).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2017 Mizzi JE et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

How to cite: Mizzi JE, Lounsberry ZT, Brown CT and Sacks BN. Draft genome of tule elk Cervus canadensis nannodes [version 2; peer review: 2 approved]. F1000Research 2017, 6:1691 (https://doi.org/10.12688/f1000research.12636.2) First published: 15 Sep 2017, 6:1691 (https://doi.org/10.12688/f1000research.12636.1) Latest published: 11 Dec 2017, 6:1691 (https://doi.org/10.12688/f1000research.12636.2)

Revised Amendments from Version 1

In this version, the name Cervus elaphus nannodes was changed to Cervus canadensis nannoodes everywhere it appeared in the publication because most people now refer to the elk as Cervus canadensis to differentiate it from Eurasian red deer. Our original publication stated that we were presenting the first Cervidae genome, but this statement has been edited to reflect the recent addition (since our initial submission) of a red deer genome Cervus elaphus hippelaphus available on NCBI. Reference 1 has also been updated to point to this genome. The reported code in the “Bioinformatics processing” section contained an erroneous “SLIDING” parameter for trimmomatic, and this has been deleted to match the correct code on GitHub. Additional information about the quality of the sequencing run was added to the Results. Table 1 was reformatted for easier viewing.

See the authors' detailed response to the review by Rudiger Brauning
See the authors' detailed response to the review by Steve Olsen

Introduction

At the initiation of this project, no genome assembly existed for any member of the deer family (Cerivdae). We therefore sought to generate the first such assembly for the tule elk (Cervus canadensis nannodes). We note that after we completed our project and submitted the intial draft of this manuscript, a full assembly of red deer (Cervus elaphus hippelaphus) became available online¹. The present paper presents the first de novo genomic draft of the tule elk. This California-endemic elk subspecies underwent a major genetic bottleneck when its numbers were reduced to as few as three individuals in the 1870s^2,3. Although their numbers have increased to >5,000 today⁴, the historical bottleneck nevertheless left its mark on the elk’s genome, rendering it more homozygous than other elk subspecies.

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 bacteria⁵.

Methods

Sample collection and library prep

Elk were selected from four geographically distinct populations across northern California to maximize genomic diversity (San Luis Reservoir, California Valley, American Canyon, and the San Luis National Wildlife Refuge⁴). Genomic DNA was extracted from skin biopsies, which were obtained by the California Department of Fish and Wildlife as part of their elk management activities⁴. We extracted DNA from skin using Qiagen DNeasy blood & tissue kits (QIAGEN Inc., Valencia, CA), according to the manufacturer’s instructions. The DNA was then fragmented via sonication using a Bioruptor (Diagenode, Denville, NJ) to 300 to 400 base pairs (bp) prior to adapter ligation. After verification of fragment size range using agarose gel electrophoresis, NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, Inc., Ipswich, MA) was used to ligate Illumina adapters. Multiplexed libraries were prepared using NEBNext Multiplex Oligos for Illumina (New England Biolabs) to individually barcode each of four individual elk. Barcodes were annealed using low-cycle polymerase chain reactions during library preparation. To assess library quality, trace analysis was performed using a Bioanalyzer 2100 (Agilent, Santa Clara, CA) and fluorometric DNA quantitation of libraries was performed using a Qubit fluorometer (Invitrogen, Carlsbad, CA) prior to equilibrating sample concentrations and pooling for sequencing. After library quality control, the four samples were pooled in equimolar concentrations and submitted for paired-end sequencing. Samples were sequenced on an Illumina HiSeq 3000 at the DNA Technologies and Expression Analysis Core of the UC Davis Genome Center.

Bioinformatics processing

Sequencing quality on demultiplexed reads was evaluated using FastQC v0.11.3 (RRID:SCR_014583)⁶. The Illumina TruSeq3-PE sequencing adapters were removed using Trimmomatic v0.30 (RRID:SCR_011848)⁷ with the ILLUMINACLIP parameter set to TruSeq3-PE.fa:2:40:15. The TruSeq3-PE.fa sequence was downloaded from https://anonscm.debian.org/cgit/debian-med/trimmomatic.git/plain/adapters/TruSeq3-PE.fa. LEADING and TRAILING parameters were set to 2, resulting in the removal of bases with a quality score of 2 or less according to a phred33 quality scoring matrix. The SLIDINGWINDOW parameter of 4:2 was used to clip reads once the quality score fell below 2 within the window. The MINLENGTH parameter set to 25 dropped any reads that fell below that length due to quality trimming. The demultiplexed, quality-filtered reads were interleaved using the interleave-reads.py script in khmer v2.0 (RRID:SCR_001156)⁸. The assembly was performed using MEGAHIT v1.0.5⁹ on interleaved quality filtered reads. Genome statistical analysis was done using QUAST v3.0 (RRID:SCR_001228)¹⁰. All code used is publicly available at https://github.com/dib-lab/2017-tule-elk/.

Results

We obtained 377,980,276 demultiplexed 150 bp paired-end raw reads, containing a total of 113.394 Gbp of sequence, from which 99.830 Gbp (88%) had quality scores ≥ Q30 (average quality score = 37.2), or approximately 40X coverage of the approximately 3 Gbp tule elk genome. Sequence assembly resulted in the generation of a total genome sequence size of 2.395 Gbp. Reads were assembled into 602,862 contiguous sequences ("contigs") averaging 3,973 bp in length with a minimum contig length of 201 bp. The G+C content of the genome was 41.55%. The N50 was 6,885 bp and maximum contig length was 72,391 bp. Additional assembly statistics are available in Table 1. No contigs (e.g. under a certain size or likely to reflect repeats) were removed from the assembly.

Table 1. Quality metrics on tule elk (Cervus canadensis nannodes) assembly, as generated with QUAST v3.0.

Metric	Tule elk assembly
# contigs (≥ 200 bp)	1,367,218
# contigs ≥ 500 bp	602,862
# contigs (≥ 1000 bp)	460,702
# contigs (≥ 5000 bp)	160,229
# contigs (≥ 10000 bp)	51,790
# contigs (≥ 25000 bp)	2,606
# contigs (≥ 50000 bp)	36
Total length (≥ 200 bp)	2,607,088,486
Total length (≥ 1000 bp)	2,295,163,580
Total length (≥ 5000 bp)	1,531,314,985
Total length (≥ 10000 bp)	771,863,493
Total length (≥ 25000 bp)	80,157,993
Total length (≥ 50000 bp)	2,056,962
Largest contig	72,391
Total length	2,395,105,945
GC	41.55%
N50	6,885
N75	3,646
L50	103,346
L75	222,107
# N's per 100 kbp	0

This genome can serve as the basis for further genomic work on tule elk and other cervids, such as the development of a SNP assay to track elk population movement across increasingly developed northern Californian terrain. Furthermore, it is one of the first whole genome assemblies available from the family Cervidae, providing a useful interim reference genome for bioinformatic analyses on other deer and elk species.

Data availability

Raw reads are available in the SRA under the BioProject ID PRJNA345218. The genome draft is available at https://doi.org/10.6084/m9.figshare.5382565.v1¹¹.

Code used in this study have been archived at http://doi.org/10.5281/zenodo.887935¹²

Competing interests

No competing interests were disclosed.

Grant information

Support for this project was provided by a grant to BNS from the California Department of Fish and Wildlife, FY1516 Big Game Management Program (Grant ID P1580009).

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Acknowledgements

JM would like to thank Luiz Irber, Camille Scott, and Lisa Johnson of the DIB lab at UC Davis for assistance with bioinformatics processing. We also thank C. Langner and J. Hobbs of the California Department of Fish and Wildlife for providing samples.

F1000 recommended

References

1. https://www.ncbi.nlm.nih.gov/genome/10790, accessed 11/29/17.
2. McCullough DR: The Tule Elk: Its History, Behavior, and Ecology. elibrary.ru. 1969. Reference Source
3. Sacks BN, Lounsberry ZT, Kalani T, et al.: Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000. J Hered. 2016; 107(7): 666–669. PubMed Abstract | Publisher Full Text
4. Hobbs JH: Draft Conservation and Management Plan for Elk. Report to the California Department of Fish and Wildlife. 2014; 41.
5. Seitz A, Nieselt K: Improving ancient DNA genome assembly. PeerJ. 2017; 5: e3126. PubMed Abstract | Publisher Full Text | Free Full Text
6. Andrews S: FastQC: a quality control tool for high throughput sequence data. 2010. Reference Source
7. Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. PubMed Abstract | Publisher Full Text | Free Full Text
8. Crusoe MR, Alameldin HF, Awad S, et al.: The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]. F1000Res. 2015; 4: 900. PubMed Abstract | Publisher Full Text | Free Full Text
9. Li D, Luo R, Liu CM, et al.: MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016; 102: 3–11. PubMed Abstract | Publisher Full Text
10. Gurevich A, Saveliev V, Vyahhi N, et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8): 1072–75. PubMed Abstract | Publisher Full Text | Free Full Text
11. Mizzi J, Lounsberry ZT, Brown CT, et al.: Tule Elk Draft Genome. figshare. 2017. Data Source
12. Mizzi J: dib-lab/2017-tule-elk: Ready for publication. Zenodo. 2017. Data Source

Comments on this article Comments (0)

Version 2

VERSION 2 PUBLISHED 15 Sep 2017

Author details Author details

Jessica E. Mizzi
Roles: Data Curation, Formal Analysis, Software, Writing – Original Draft Preparation, Writing – Review & Editing

Zachary T. Lounsberry
Roles: Resources, Writing – Review & Editing

C. Titus Brown
Roles: Resources, Supervision, Writing – Review & Editing

Benjamin N. Sacks
Roles: Conceptualization, Funding Acquisition, Resources, Supervision, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

Support for this project was provided by a grant to BNS from the California Department of Fish and Wildlife, FY1516 Big Game Management Program (Grant ID P1580009).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Article Versions (2)

version 2

Revised

Published: 11 Dec 2017, 6:1691

https://doi.org/10.12688/f1000research.12636.2

version 1

Published: 15 Sep 2017, 6:1691

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

© 2017 Mizzi JE et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

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Mizzi JE, Lounsberry ZT, Brown CT and Sacks BN. Draft genome of tule elk Cervus canadensis nannodes [version 2; peer review: 2 approved]. F1000Research 2017, 6:1691 (https://doi.org/10.12688/f1000research.12636.2)

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Version 2

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PUBLISHED 11 Dec 2017

Revised

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Reviewer Report 18 Dec 2017

Rudiger Brauning, Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand

Approved

https://doi.org/10.5256/f1000research.14577.r28939

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PUBLISHED 15 Sep 2017

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Reviewer Report 16 Nov 2017

Rudiger Brauning, Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand

Approved with Reservations

https://doi.org/10.5256/f1000research.13682.r27606

The authors describe the generation of a draft assembly for tule elk in the style of a brief genome announcement. For SNP detection and primer design this assembly is fine. It could e.g. be used in combination with Genotyping by Sequencing on additional individuals.

Materials and methods are sound and provided in full.

However a quick search of NCBI's taxonomy resource reveals that since June 2017 there is a genome assembly for red deer available https://www.ncbi.nlm.nih.gov/genome/10790. The authors therefore cannot claim to present the first whole genome assembly from the family Cervidae. Please change that statement.

Suggested further improvements:

Results

I would have liked to see a figure for the total amount of sequence after filtering as a simple way of showing how good or bad the sequence run was.

Table 1's readability would be improved by getting all figures to align right.

I'd also recommend to add another assembly metric to look at the gene content; either using something like BUSCO or by mapping the refseq sequences of a related, well annotated species (e.g. cattle) against the draft genome.

Methods

Sample collection and library prep
I see that each individual has two tissue samples. The authors entered a sample ID into the 'tissue' field of NCBI's BioSample database. I'd recommend removing this and adding the animal ID in the 'isolate' field.

Please expand the entries in the 'isolation source' field. It says e.g. "Am. Cyn" which probably means American Canyon.

Bioinformatics processing
Checking the code I believe the statement "LEADING, TRAILING, and SLIDING parameters were set to 2" should read "LEADING and TRAILING parameters were set to 2".

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Yes

Competing Interests: No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Author Response 11 Dec 2017

Jessica Mizzi, Microbiology Graduate Group, University of California, Davis, 95616, USA

11 Dec 2017

Author Response

Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been ... Continue reading Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been made. Table 1 has been reformatted for readability. The changes you’ve requested to the NCBI BioSample entry have been made. The trimmomatic code in the Bioinformatics Processing section has been edited to remove the erroneous “SLIDING” parameter. We’ve added text to the first sentence of the results section that describes the quality of sequence data in terms of standard quality scores. We opted not to provide details on the gene content relative to a related genome as we felt this could be done more comprehensively in the future once the red deer genome has been published and peer-reviewed.
Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been made. Table 1 has been reformatted for readability. The changes you’ve requested to the NCBI BioSample entry have been made. The trimmomatic code in the Bioinformatics Processing section has been edited to remove the erroneous “SLIDING” parameter. We’ve added text to the first sentence of the results section that describes the quality of sequence data in terms of standard quality scores. We opted not to provide details on the gene content relative to a related genome as we felt this could be done more comprehensively in the future once the red deer genome has been published and peer-reviewed.
Competing Interests: I declare no competing interests. Close
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Author Response 11 Dec 2017

Jessica Mizzi, Microbiology Graduate Group, University of California, Davis, 95616, USA

11 Dec 2017

Author Response

Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been ... Continue reading Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been made. Table 1 has been reformatted for readability. The changes you’ve requested to the NCBI BioSample entry have been made. The trimmomatic code in the Bioinformatics Processing section has been edited to remove the erroneous “SLIDING” parameter. We’ve added text to the first sentence of the results section that describes the quality of sequence data in terms of standard quality scores. We opted not to provide details on the gene content relative to a related genome as we felt this could be done more comprehensively in the future once the red deer genome has been published and peer-reviewed.
Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been made. Table 1 has been reformatted for readability. The changes you’ve requested to the NCBI BioSample entry have been made. The trimmomatic code in the Bioinformatics Processing section has been edited to remove the erroneous “SLIDING” parameter. We’ve added text to the first sentence of the results section that describes the quality of sequence data in terms of standard quality scores. We opted not to provide details on the gene content relative to a related genome as we felt this could be done more comprehensively in the future once the red deer genome has been published and peer-reviewed.
Competing Interests: I declare no competing interests. Close
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Reviewer Report 25 Oct 2017

Steve Olsen, Infectious Bacterial Diseases Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA

Approved

https://doi.org/10.5256/f1000research.13682.r26607

This article describes the generation of a draft genome (40X coverage from 4 animals) of the tule elk (Cervus elaphus nannodes). The research methods are fairly standard for the Illumina sequencing used. At 602,862 contigs, the genome is very prelminary and will require quite a bit of additional work ... Continue reading

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Yes

Competing Interests: No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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Author Response 11 Dec 2017

Jessica Mizzi, Microbiology Graduate Group, University of California, Davis, 95616, USA

11 Dec 2017

Author Response

Thank you for your review of this paper.
Competing Interests: I declare no competing interests.
Thank you for your review of this paper.
Thank you for your review of this paper.
Competing Interests: I declare no competing interests. Close
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COMMENTS ON THIS REPORT

Author Response 11 Dec 2017

Jessica Mizzi, Microbiology Graduate Group, University of California, Davis, 95616, USA

11 Dec 2017

Author Response

Thank you for your review of this paper.
Competing Interests: I declare no competing interests.
Thank you for your review of this paper.
Thank you for your review of this paper.
Competing Interests: I declare no competing interests. Close
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Rudiger Brauning, Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand

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Approved

I'm happy with the changes made, no further comments.

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Rudiger Brauning, Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand

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Approved With Reservations

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Yes

Competing Interests

No competing interests were disclosed.

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11 Dec 2017

Jessica Mizzi, Microbiology Graduate Group, University of California, Davis, 95616, USA

Thank you for your review of this paper. Version 2 has been edited to reflect the presence of the red deer genome and a citation to that genome has been made. Table 1 has been reformatted for readability. The changes you’ve requested to the NCBI BioSample entry have been made. The trimmomatic code in the Bioinformatics Processing section has been edited to remove the erroneous “SLIDING” parameter. We’ve added text to the first sentence of the results section that describes the quality of sequence data in terms of standard quality scores. We opted not to provide details on the gene content relative to a related genome as we felt this could be done more comprehensively in the future once the red deer genome has been published and peer-reviewed.

View more View less

Competing Interests

I declare no competing interests.

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25 Oct 2017 | for Version 1

Steve Olsen, Infectious Bacterial Diseases Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA

20 Views Cite this report Responses(1)

Approved

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Yes

Competing Interests

No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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Alongside their report, reviewers assign a status to the article:

Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions

[1] 1. https://www.ncbi.nlm.nih.gov/genome/10790, accessed 11/29/17.

[2] 2. McCullough DR: The Tule Elk: Its History, Behavior, and Ecology. elibrary.ru. 1969. Reference Source

[3] 3. Sacks BN, Lounsberry ZT, Kalani T, et al.: Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000. J Hered. 2016; 107(7): 666–669. PubMed Abstract | Publisher Full Text

[4] 4. Hobbs JH: Draft Conservation and Management Plan for Elk. Report to the California Department of Fish and Wildlife. 2014; 41.

[5] 5. Seitz A, Nieselt K: Improving ancient DNA genome assembly. PeerJ. 2017; 5: e3126. PubMed Abstract | Publisher Full Text | Free Full Text

[6] 6. Andrews S: FastQC: a quality control tool for high throughput sequence data. 2010. Reference Source

[7] 7. Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. PubMed Abstract | Publisher Full Text | Free Full Text

[8] 8. Crusoe MR, Alameldin HF, Awad S, et al.: The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]. F1000Res. 2015; 4: 900. PubMed Abstract | Publisher Full Text | Free Full Text

[9] 9. Li D, Luo R, Liu CM, et al.: MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016; 102: 3–11. PubMed Abstract | Publisher Full Text

[10] 10. Gurevich A, Saveliev V, Vyahhi N, et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8): 1072–75. PubMed Abstract | Publisher Full Text | Free Full Text

[11] 11. Mizzi J, Lounsberry ZT, Brown CT, et al.: Tule Elk Draft Genome. figshare. 2017. Data Source

[12] 12. Mizzi J: dib-lab/2017-tule-elk: Ready for publication. Zenodo. 2017. Data Source

Draft genome of tule elk Cervus canadensis nannodes

Abstract

Keywords

Revised Amendments from Version 1

Introduction

Methods

Sample collection and library prep

Bioinformatics processing

Results

Table 1. Quality metrics on tule elk (Cervus canadensis nannodes) assembly, as generated with QUAST v3.0.

Data availability

Competing interests

Grant information

Acknowledgements

References

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