De novo sequencing and initial annotation of the Mongolian gerbil (Meriones unguiculatus) genome

Zorio, Diego A. R.; Monsma, Scott; Sanes, Dan H.; Golding, Nace L.; Rubel, Edwin W.; Wang, Yuan

doi:10.1016/j.ygeno.2018.03.001

Cited by 36 publications

(39 citation statements)

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“…To calculate the standardised average coverage for males and females, we divided all read counts for each individual by the sequencing effort of that individual, multiplied by 1,000,000, and then took the mean of all males and all females. Y linked markers fulfil the inequality: Then we used blastn to align each marker to the gerbil genome GCF_002204375.1_MunDraft-v1.0_genomic.fna (Zorio et al 2018). Once markers were aligned to the genome we annotated sex-linked scaffolds and tested how often a single genomic scaffold associated with multiple different linkage groups as these cases indicate chimeric scaffolds.…”

Section: Scaffolding the Genomementioning

confidence: 99%

“…We annotated 421,257 autosomal stacks, 11,322 X-linked stacks, 5,110 Y-linked stacks, and 14,505 unknown stacks by analysing the relative coverage of males and females (Figure 2). By aligning these stacks to the published genome (Zorio et al 2018), we annotated 17,121 autosomal scaffolds (2,246,217,465…”

Section: Genetic Mapmentioning

confidence: 99%

“…While a great deal of cytological research has been done on various gerbils (Cohen 1970;Benazzou et al 1982), there has been no bridge yet between the new genomics era and these classic karyotype studies. Three gerbil species (Mongolian gerbils, fat sandrats, and great gerbils) have all recently had their genomes sequenced (Hargreaves et al 2017;Zorio et al 2018;Nilsson et al 2018). But as yet, none of these genomes are complete and all assemblies are highly fragmented.…”

mentioning

confidence: 99%

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A high-density genetic map and molecular sex-typing assay for gerbils

Brekke

Supriya

Denver

et al. 2019

Preprint

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We constructed a high-density genetic map in Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a twostep approach. First, we chose the highest-quality set of 485 markers to construct a high-quality framework map of 1,239cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5,449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1,140 genomic scaffolds (containing ~20% of annotated genes) into a chromosome-level framework. We used both genetic linkage and relative sequencing coverage in males and females to identify X-and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is not possible using current visual methods.

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Section: Scaffolding the Genomementioning

confidence: 99%

Section: Genetic Mapmentioning

confidence: 99%

mentioning

confidence: 99%

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A high-density genetic map and molecular sex-typing assay for gerbils

Brekke

Supriya

Denver

et al. 2019

Preprint

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“…Here we describe a de novo assembly and annotation of the Mongolian gerbil genome and transcriptome. Recently, a separate group has sequenced the gerbil genome, however our work is further supported by comparisons with an in-depth transcriptome analysis, which was not performed by the previous group (10). RNA-seq data were produced from 27 tissues that were used in the genome annotation and deposited in the China National GeneBank CNSA repository under the project CNP0000340andNCBI Bioproject # SRP198569, SRA887264, PRJNA543000.…”

Section: Introductionmentioning

confidence: 99%

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

Cheng

Zhang

et al. 2019

Preprint

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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 sequenced using Illumina HiSeq 2000 and after assembly 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 the first de novo assembly of the Mongolian gerbil genome enhanced by assembly of transcriptome data from several tissues. Sequencing of this genome and transcriptome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools.

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“…While a great deal of cytological research has been done on various gerbils (Cohen 1970 ; Benazzou et al 1982 ), there has been no bridge yet between the new genomics era and these classic karyotype studies. Three gerbil species (Mongolian gerbils, fat sandrats, and great gerbils) have all recently had their genomes sequenced (Hargreaves et al 2017 ; Zorio et al 2018 ; Nilsson et al 2018 ). But as yet, none of these genomes are complete and all assemblies are highly fragmented.…”

mentioning

confidence: 99%

A high-density genetic map and molecular sex-typing assay for gerbils

et al. 2019

View full text Add to dashboard Cite

We constructed a high-density genetic map for Mongolian gerbils ( Meriones unguiculatus ). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus : 10047. Electronic supplementary material The online version of this article (10.1007/s00335-019-09799-z) contains supplementary material, which is available to authorized users.

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De novo sequencing and initial annotation of the Mongolian gerbil (Meriones unguiculatus) genome

Cited by 36 publications

References 100 publications

A high-density genetic map and molecular sex-typing assay for gerbils

A high-density genetic map and molecular sex-typing assay for gerbils

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

A high-density genetic map and molecular sex-typing assay for gerbils

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