Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals
Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species.Aiming at characterizing SDs across the genomes o...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2017
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/129506 |
| _version_ | 1855534563268231168 |
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| author | Xiaotian Feng Jicai Jiang Padhi, Abinash Chao Ning Jinluan Fu Aiguo Wang Mrode, Raphael A. Jian-Feng Liu |
| author_browse | Aiguo Wang Chao Ning Jian-Feng Liu Jicai Jiang Jinluan Fu Mrode, Raphael A. Padhi, Abinash Xiaotian Feng |
| author_facet | Xiaotian Feng Jicai Jiang Padhi, Abinash Chao Ning Jinluan Fu Aiguo Wang Mrode, Raphael A. Jian-Feng Liu |
| author_sort | Xiaotian Feng |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species.Aiming at characterizing SDs across the genomes of diverse livestock species, we mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken, and also enhanced the existing SD maps of cattle and pig genomes based on the most updated genome assemblies. We adopted two different detection strategies, whole genome analysis comparison and whole genome shotgun sequence detection, to pursue more convincing findings. Accordingly we identified SDs for each species with the length of from 21.7 Mb to 164.1 Mb, and 807 to 4,560 genes were harboured within the SD regions across different species. More interestingly, many of these SD-related genes were involved in the process of immunity and response to external stimuli. We also found the existence of 59 common genes within SD regions in all studied species except goat. These common genes mainly consisted of both UDP glucuronosyltransferase and Interferon alpha families, implying the connection between SDs and the evolution of these gene families.Our findings provide insights into livestock genome evolution and offer rich genomic sources for livestock genomic research. |
| format | Journal Article |
| id | CGSpace129506 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1295062024-10-03T07:40:58Z Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals Xiaotian Feng Jicai Jiang Padhi, Abinash Chao Ning Jinluan Fu Aiguo Wang Mrode, Raphael A. Jian-Feng Liu immunity domestic animals animals association Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species.Aiming at characterizing SDs across the genomes of diverse livestock species, we mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken, and also enhanced the existing SD maps of cattle and pig genomes based on the most updated genome assemblies. We adopted two different detection strategies, whole genome analysis comparison and whole genome shotgun sequence detection, to pursue more convincing findings. Accordingly we identified SDs for each species with the length of from 21.7 Mb to 164.1 Mb, and 807 to 4,560 genes were harboured within the SD regions across different species. More interestingly, many of these SD-related genes were involved in the process of immunity and response to external stimuli. We also found the existence of 59 common genes within SD regions in all studied species except goat. These common genes mainly consisted of both UDP glucuronosyltransferase and Interferon alpha families, implying the connection between SDs and the evolution of these gene families.Our findings provide insights into livestock genome evolution and offer rich genomic sources for livestock genomic research. 2017-12 2023-03-10T14:37:11Z 2023-03-10T14:37:11Z Journal Article https://hdl.handle.net/10568/129506 en Open Access Springer Feng, Xiaotian; Jiang, Jicai; Padhi, Abinash; Ning, Chao; Fu, Jinluan; Wang, Aiguo; Mrode, Raphael A.; Liu, Jian-Feng. 2017. Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals. BMC Genomics 18: |
| spellingShingle | immunity domestic animals animals association Xiaotian Feng Jicai Jiang Padhi, Abinash Chao Ning Jinluan Fu Aiguo Wang Mrode, Raphael A. Jian-Feng Liu Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title | Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title_full | Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title_fullStr | Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title_full_unstemmed | Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title_short | Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| title_sort | characterization of genome wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals |
| topic | immunity domestic animals animals association |
| url | https://hdl.handle.net/10568/129506 |
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