Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing
The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcript...
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MDPI AG
2022-08-01
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| author | Pengfei Hu Zhen Wang Jiping Li Dongxu Wang Yusu Wang Quanmin Zhao Chunyi Li |
| author_facet | Pengfei Hu Zhen Wang Jiping Li Dongxu Wang Yusu Wang Quanmin Zhao Chunyi Li |
| author_sort | Pengfei Hu |
| collection | DOAJ |
| description | The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely <i>RNA Binding Motif Protein X-Linked (RBMX)</i> and <i>methyltransferase-like 3 (METTL3)</i>, respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate. |
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| language | English |
| last_indexed | 2024-03-10T03:07:53Z |
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| spelling | doaj.art-bd4b4b351302473c87eed9399c1062a42023-11-23T12:36:57ZengMDPI AGAnimals2076-26152022-08-011217220310.3390/ani12172203Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome SequencingPengfei Hu0Zhen Wang1Jiping Li2Dongxu Wang3Yusu Wang4Quanmin Zhao5Chunyi Li6Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaCollege of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, ChinaThe molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely <i>RNA Binding Motif Protein X-Linked (RBMX)</i> and <i>methyltransferase-like 3 (METTL3)</i>, respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate.https://www.mdpi.com/2076-2615/12/17/2203antler growth ratealternative splicing variantspositive selection genessingle molecule real time sequencingcomparative transcriptome |
| spellingShingle | Pengfei Hu Zhen Wang Jiping Li Dongxu Wang Yusu Wang Quanmin Zhao Chunyi Li Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing Animals antler growth rate alternative splicing variants positive selection genes single molecule real time sequencing comparative transcriptome |
| title | Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing |
| title_full | Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing |
| title_fullStr | Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing |
| title_full_unstemmed | Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing |
| title_short | Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing |
| title_sort | identification and characterization of alternative splicing variants and positive selection genes related to distinct growth rates of antlers using comparative transcriptome sequencing |
| topic | antler growth rate alternative splicing variants positive selection genes single molecule real time sequencing comparative transcriptome |
| url | https://www.mdpi.com/2076-2615/12/17/2203 |
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