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Research article

Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues

Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Lu, Xun Xu, Achim Klug, Elizabeth McCullagh
DOI: 10.21203/rs.2.12749/v1

Abstract

BACKGROUND: The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome sequencing and assembly from 27 different tissues samples. RESULTS: The genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 31 769 (>2000bp) predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONS: We report a de novo assembly of the Mongolian gerbil genome that was further enhanced by assembly of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.

Keywords
Gerbil genome, Meriones unguiculatus, transcriptome, model organism

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BACKGROUND

RESULTS

DISCUSSION

CONCLUSIONS

METHODS

List of abbreviations

DECLARATIONS

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Preprint: Please note that this article has not completed peer review.
Research article

Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues

Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Lu, Xun Xu, Achim Klug, Elizabeth McCullagh

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Abstract

BACKGROUND: The Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome sequencing and assembly from 27 different tissues samples. RESULTS: The genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 31 769 (>2000bp) predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONS: We report a de novo assembly of the Mongolian gerbil genome that was further enhanced by assembly of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.

Figures

BACKGROUND

RESULTS

DISCUSSION

CONCLUSIONS

METHODS

List of abbreviations

DECLARATIONS

References

Tables

Learn more about our company.