Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues
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 r...
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| Format: | Article |
| Language: | English |
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BMC
2019-11-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6276-y |
| _version_ | 1818858718358405120 |
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| author | Shifeng Cheng Yuan Fu Yaolei Zhang Wenfei Xian Hongli Wang Benedikt Grothe Xin Liu Xun Xu Achim Klug Elizabeth A. McCullagh |
| author_facet | Shifeng Cheng Yuan Fu Yaolei Zhang Wenfei Xian Hongli Wang Benedikt Grothe Xin Liu Xun Xu Achim Klug Elizabeth A. McCullagh |
| author_sort | Shifeng Cheng |
| collection | DOAJ |
| description | 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 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 (> 2000 bp) 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. |
| first_indexed | 2024-12-19T09:00:44Z |
| format | Article |
| id | doaj.art-28f56803c3814f79b52bb66feeba9346 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T09:00:44Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-28f56803c3814f79b52bb66feeba93462022-12-21T20:28:28ZengBMCBMC Genomics1471-21642019-11-012011610.1186/s12864-019-6276-yEnhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissuesShifeng Cheng0Yuan Fu1Yaolei Zhang2Wenfei Xian3Hongli Wang4Benedikt Grothe5Xin Liu6Xun Xu7Achim Klug8Elizabeth A. McCullagh9BGI-Shenzhen, Beishan Industrial ZoneBGI-Shenzhen, Beishan Industrial ZoneBGI-Shenzhen, Beishan Industrial ZoneBGI-Shenzhen, Beishan Industrial ZoneBGI-Shenzhen, Beishan Industrial ZoneDivision of Neurobiology, Ludwig-Maximilians-Universitaet MunichBGI-Shenzhen, Beishan Industrial ZoneBGI-Shenzhen, Beishan Industrial ZoneDepartment of Physiology and Biophysics, School of Medicine, University of Colorado DenverDepartment of Physiology and Biophysics, School of Medicine, University of Colorado DenverAbstract 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 (> 2000 bp) 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.http://link.springer.com/article/10.1186/s12864-019-6276-yGerbil genomeMeriones unguiculatusTranscriptomeModel organism |
| spellingShingle | Shifeng Cheng Yuan Fu Yaolei Zhang Wenfei Xian Hongli Wang Benedikt Grothe Xin Liu Xun Xu Achim Klug Elizabeth A. McCullagh Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues BMC Genomics Gerbil genome Meriones unguiculatus Transcriptome Model organism |
| title | Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| title_full | Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| title_fullStr | Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| title_full_unstemmed | Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| title_short | Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| title_sort | enhancement of de novo sequencing assembly and annotation of the mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues |
| topic | Gerbil genome Meriones unguiculatus Transcriptome Model organism |
| url | http://link.springer.com/article/10.1186/s12864-019-6276-y |
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