Identification of avian W-linked contigs by short-read sequencing
Background: The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identi...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2012
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| Online Access: | http://hdl.handle.net/1721.1/72993 https://orcid.org/0000-0001-9920-3411 |
| _version_ | 1811084958124474368 |
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| author | Chen, Nancy Bellott, Daniel W. Clark, Andrew G Page, David C |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Chen, Nancy Bellott, Daniel W. Clark, Andrew G Page, David C |
| author_sort | Chen, Nancy |
| collection | MIT |
| description | Background: The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identifying sequences that are W-specific. Results: Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 60 novel W-specific sequences. Conclusions: Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution. |
| first_indexed | 2024-09-23T13:00:44Z |
| format | Article |
| id | mit-1721.1/72993 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:00:44Z |
| publishDate | 2012 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/729932022-09-28T11:26:54Z Identification of avian W-linked contigs by short-read sequencing Chen, Nancy Bellott, Daniel W. Clark, Andrew G Page, David C Massachusetts Institute of Technology. Department of Biology Whitehead Institute for Biomedical Research Page, David C. Bellott, Daniel W. Background: The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identifying sequences that are W-specific. Results: Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 60 novel W-specific sequences. Conclusions: Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution. National Institutes of Health (U.S.) (NIH grant R01 GM64590) National Science Foundation (U.S.) (Graduate Research Fellowship) 2012-09-17T15:43:29Z 2012-09-17T15:43:29Z 2012-05 2011-12 2012-08-28T11:17:08Z Article http://purl.org/eprint/type/JournalArticle 1471-2164 http://hdl.handle.net/1721.1/72993 Chen, Nancy et al. “Identification of Avian W-linked Contigs by Short-read Sequencing.” BMC Genomics 13.1 (2012): 183. Web. https://orcid.org/0000-0001-9920-3411 en http://dx.doi.org/10.1186/1471-2164-13-183 BMC Genomics Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Nancy Chen et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Chen, Nancy Bellott, Daniel W. Clark, Andrew G Page, David C Identification of avian W-linked contigs by short-read sequencing |
| title | Identification of avian W-linked contigs by short-read sequencing |
| title_full | Identification of avian W-linked contigs by short-read sequencing |
| title_fullStr | Identification of avian W-linked contigs by short-read sequencing |
| title_full_unstemmed | Identification of avian W-linked contigs by short-read sequencing |
| title_short | Identification of avian W-linked contigs by short-read sequencing |
| title_sort | identification of avian w linked contigs by short read sequencing |
| url | http://hdl.handle.net/1721.1/72993 https://orcid.org/0000-0001-9920-3411 |
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