Physical Mapping of 20 Unmapped Fragments of the Btau_4.0 Genome Assembly in Cattle, Sheep and River Buffalo
The recent advances in sequencing technology and bioinformatics have revolutionized genomic research, making the decoding of the genome an easier task. Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accur...
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| Veröffentlicht in: | Cytogenetic and genome research 2013-01, Vol.140 (1), p.29-35 |
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| creator | De Lorenzi, L. Genualdo, V. Perucatti, A. Iannuzzi, A. Iannuzzi, L. Parma, P. |
| description | The recent advances in sequencing technology and bioinformatics have revolutionized genomic research, making the decoding of the genome an easier task. Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (Bos taurus, 2n = 60), sheep (Ovis aries, 2n = 54) and river buffalo (Bubalus bubalis, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. Finally, the results presented here suggest that FISH was, and still is, a useful technology to validate the data produced by genome sequencing programs. |
| doi_str_mv | 10.1159/000350869 |
| format | Article |
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Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (Bos taurus, 2n = 60), sheep (Ovis aries, 2n = 54) and river buffalo (Bubalus bubalis, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. 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Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (Bos taurus, 2n = 60), sheep (Ovis aries, 2n = 54) and river buffalo (Bubalus bubalis, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. Finally, the results presented here suggest that FISH was, and still is, a useful technology to validate the data produced by genome sequencing programs.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Bos taurus</subject><subject>Bubalus bubalis</subject><subject>Buffaloes - genetics</subject><subject>Cattle - genetics</subject><subject>Chromosomes, Artificial, Bacterial - genetics</subject><subject>Chromosomes, Mammalian - genetics</subject><subject>Databases, Genetic</subject><subject>Genetic Loci</subject><subject>Genome</subject><subject>In Situ Hybridization, Fluorescence</subject><subject>Interleukin-13 Receptor alpha2 Subunit - genetics</subject><subject>Original Article</subject><subject>Ovis aries</subject><subject>Physical Chromosome Mapping - methods</subject><subject>Reproducibility of Results</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Sheep - genetics</subject><subject>Species Specificity</subject><issn>1424-8581</issn><issn>1424-859X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqN0ctr3DAQB2BRWppk00PvpQh6SSGbjJ6Wj8mSFyQkpA30ZmR5tOvUr0p2Yf_7KOx2Dz3lNCP0aRjxI-QzgxPGVH4KAEKB0fk7ss8kl3Oj8l_vd71he-QgxmcAZqTSH8keF1rx3Mh90jys1rF2tqF3dhjqbkl7TznQp65NZ6zoZbDLFrsxvl6MK6Tno50KeQL0Cru-RXoWI7Zls6Z1Rxd2HBs8pj9WiAO1XUUf678Y6PnkvW36Q_IhlYiftnVGni4vfi6u57f3VzeLs9u5Ezob5xVUXBhhGfMVgFSl81YLJyzPPQc0vOSpd95ILZBbj8bpzORaCV16x1HMyNFm7hD6PxPGsWjr6LBpbIf9FAsmMg6KaZG9garEQEKe6Lf_6HM_hS59pGCSmSztnEbOyPeNcqGPMaAvhlC3NqwLBsVrWsUurWS_bidOZYvVTv6LJ4EvG_DbhiWGHdi-fwFHSZUs</recordid><startdate>20130101</startdate><enddate>20130101</enddate><creator>De Lorenzi, L.</creator><creator>Genualdo, V.</creator><creator>Perucatti, A.</creator><creator>Iannuzzi, A.</creator><creator>Iannuzzi, L.</creator><creator>Parma, P.</creator><general>S. 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Genualdo, V. ; Perucatti, A. ; Iannuzzi, A. ; Iannuzzi, L. ; Parma, P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c367t-d0d2383a11fd0045bcfa63c3a29f20e82b23a2cf8463e2afe8c67896536bfc2e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Bos taurus</topic><topic>Bubalus bubalis</topic><topic>Buffaloes - genetics</topic><topic>Cattle - genetics</topic><topic>Chromosomes, Artificial, Bacterial - genetics</topic><topic>Chromosomes, Mammalian - genetics</topic><topic>Databases, Genetic</topic><topic>Genetic Loci</topic><topic>Genome</topic><topic>In Situ Hybridization, Fluorescence</topic><topic>Interleukin-13 Receptor alpha2 Subunit - genetics</topic><topic>Original Article</topic><topic>Ovis aries</topic><topic>Physical Chromosome Mapping - methods</topic><topic>Reproducibility of Results</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Sheep - genetics</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>De Lorenzi, L.</creatorcontrib><creatorcontrib>Genualdo, V.</creatorcontrib><creatorcontrib>Perucatti, A.</creatorcontrib><creatorcontrib>Iannuzzi, A.</creatorcontrib><creatorcontrib>Iannuzzi, L.</creatorcontrib><creatorcontrib>Parma, P.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><jtitle>Cytogenetic and genome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>De Lorenzi, L.</au><au>Genualdo, V.</au><au>Perucatti, A.</au><au>Iannuzzi, A.</au><au>Iannuzzi, L.</au><au>Parma, P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Physical Mapping of 20 Unmapped Fragments of the Btau_4.0 Genome Assembly in Cattle, Sheep and River Buffalo</atitle><jtitle>Cytogenetic and genome research</jtitle><addtitle>Cytogenet Genome Res</addtitle><date>2013-01-01</date><risdate>2013</risdate><volume>140</volume><issue>1</issue><spage>29</spage><epage>35</epage><pages>29-35</pages><issn>1424-8581</issn><eissn>1424-859X</eissn><abstract>The recent advances in sequencing technology and bioinformatics have revolutionized genomic research, making the decoding of the genome an easier task. Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (Bos taurus, 2n = 60), sheep (Ovis aries, 2n = 54) and river buffalo (Bubalus bubalis, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. Finally, the results presented here suggest that FISH was, and still is, a useful technology to validate the data produced by genome sequencing programs.</abstract><cop>Basel, Switzerland</cop><pub>S. Karger AG</pub><pmid>23652984</pmid><doi>10.1159/000350869</doi><tpages>7</tpages></addata></record> |
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| ispartof | Cytogenetic and genome research, 2013-01, Vol.140 (1), p.29-35 |
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| source | Karger Journals; MEDLINE; Alma/SFX Local Collection |
| subjects | Animals Base Sequence Bos taurus Bubalus bubalis Buffaloes - genetics Cattle - genetics Chromosomes, Artificial, Bacterial - genetics Chromosomes, Mammalian - genetics Databases, Genetic Genetic Loci Genome In Situ Hybridization, Fluorescence Interleukin-13 Receptor alpha2 Subunit - genetics Original Article Ovis aries Physical Chromosome Mapping - methods Reproducibility of Results Sequence Homology, Nucleic Acid Sheep - genetics Species Specificity |
| title | Physical Mapping of 20 Unmapped Fragments of the Btau_4.0 Genome Assembly in Cattle, Sheep and River Buffalo |
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