Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes
The Great Himalayan Leaf-nosed bat (<i>Hipposideros armiger</i>) is one of the most representative species of all echolocating bats and is an ideal model for studying the echolocation system of bats. An incomplete reference genome and limited availability of full-length cDNAs have hinder...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/5/4937 |
| _version_ | 1797615110460538880 |
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| author | Mingyue Bao Xue Wang Ruyi Sun Zhiqiang Wang Jiqian Li Tinglei Jiang Aiqing Lin Hui Wang Jiang Feng |
| author_facet | Mingyue Bao Xue Wang Ruyi Sun Zhiqiang Wang Jiqian Li Tinglei Jiang Aiqing Lin Hui Wang Jiang Feng |
| author_sort | Mingyue Bao |
| collection | DOAJ |
| description | The Great Himalayan Leaf-nosed bat (<i>Hipposideros armiger</i>) is one of the most representative species of all echolocating bats and is an ideal model for studying the echolocation system of bats. An incomplete reference genome and limited availability of full-length cDNAs have hindered the identification of alternatively spliced transcripts, which slowed down related basic studies on bats’ echolocation and evolution. In this study, we analyzed five organs from <i>H. armiger</i> for the first time using PacBio single-molecule real-time sequencing (SMRT). There were 120 GB of subreads generated, including 1,472,058 full-length non-chimeric (FLNC) sequences. A total of 34,611 alternative splicing (AS) events and 66,010 Alternative Polyadenylation (APA) sites were detected by transcriptome structural analysis. Moreover, a total of 110,611 isoforms were identified, consisting of 52% new isoforms of known genes and 5% of novel gene loci, as well as 2112 novel genes that have not been annotated before in the current reference genome of <i>H. armiger</i>. Furthermore, several key novel genes, including <i>Pol</i>, <i>RAS</i>, <i>NFKB1</i>, and <i>CAMK4</i>, were identified as being associated with nervous, signal transduction, and immune system processes, which may be involved in regulating the auditory nervous perception and immune system that helps bats to regulate in echolocation. In conclusion, the full-length transcriptome results optimized and replenished existing <i>H. armiger</i> genome annotation in multiple ways and offer advantages for newly discovered or previously unrecognized protein-coding genes and isoforms, which can be used as a reference resource. |
| first_indexed | 2024-03-11T07:21:52Z |
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| id | doaj.art-b7b4f476ac6d4d94868e675c49293706 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T07:21:52Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-b7b4f476ac6d4d94868e675c492937062023-11-17T07:55:28ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01245493710.3390/ijms24054937Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel GenesMingyue Bao0Xue Wang1Ruyi Sun2Zhiqiang Wang3Jiqian Li4Tinglei Jiang5Aiqing Lin6Hui Wang7Jiang Feng8College of Life Science, Jilin Agricultural University, Changchun 130118, ChinaCollege of Life Science, Jilin Agricultural University, Changchun 130118, ChinaCollege of Life Science, Jilin Agricultural University, Changchun 130118, ChinaJilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, ChinaJilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, ChinaJilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, ChinaJilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, ChinaCollege of Life Science, Jilin Agricultural University, Changchun 130118, ChinaCollege of Life Science, Jilin Agricultural University, Changchun 130118, ChinaThe Great Himalayan Leaf-nosed bat (<i>Hipposideros armiger</i>) is one of the most representative species of all echolocating bats and is an ideal model for studying the echolocation system of bats. An incomplete reference genome and limited availability of full-length cDNAs have hindered the identification of alternatively spliced transcripts, which slowed down related basic studies on bats’ echolocation and evolution. In this study, we analyzed five organs from <i>H. armiger</i> for the first time using PacBio single-molecule real-time sequencing (SMRT). There were 120 GB of subreads generated, including 1,472,058 full-length non-chimeric (FLNC) sequences. A total of 34,611 alternative splicing (AS) events and 66,010 Alternative Polyadenylation (APA) sites were detected by transcriptome structural analysis. Moreover, a total of 110,611 isoforms were identified, consisting of 52% new isoforms of known genes and 5% of novel gene loci, as well as 2112 novel genes that have not been annotated before in the current reference genome of <i>H. armiger</i>. Furthermore, several key novel genes, including <i>Pol</i>, <i>RAS</i>, <i>NFKB1</i>, and <i>CAMK4</i>, were identified as being associated with nervous, signal transduction, and immune system processes, which may be involved in regulating the auditory nervous perception and immune system that helps bats to regulate in echolocation. In conclusion, the full-length transcriptome results optimized and replenished existing <i>H. armiger</i> genome annotation in multiple ways and offer advantages for newly discovered or previously unrecognized protein-coding genes and isoforms, which can be used as a reference resource.https://www.mdpi.com/1422-0067/24/5/4937<i>Hipposideros armiger</i>full-length transcriptomePacBiogenome annotationSMRT sequencing |
| spellingShingle | Mingyue Bao Xue Wang Ruyi Sun Zhiqiang Wang Jiqian Li Tinglei Jiang Aiqing Lin Hui Wang Jiang Feng Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes International Journal of Molecular Sciences <i>Hipposideros armiger</i> full-length transcriptome PacBio genome annotation SMRT sequencing |
| title | Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes |
| title_full | Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes |
| title_fullStr | Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes |
| title_full_unstemmed | Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes |
| title_short | Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (<i>Hipposideros armiger</i>) Optimized Genome Annotation and Revealed the Expression of Novel Genes |
| title_sort | full length transcriptome of the great himalayan leaf nosed bats i hipposideros armiger i optimized genome annotation and revealed the expression of novel genes |
| topic | <i>Hipposideros armiger</i> full-length transcriptome PacBio genome annotation SMRT sequencing |
| url | https://www.mdpi.com/1422-0067/24/5/4937 |
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