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The Neurospora crassa Genome: Cosmid Libraries Sorted by Chromosome
A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for...
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| Published in: | Genetics (Austin) 2001-03, Vol.157 (3), p.979-990 |
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| cites | cdi_FETCH-LOGICAL-c456t-b2ef6dbd68c2b1bc10cdb54f9cec8bc5333f1560a4db478a8dbee343f4a6e78f3 |
| container_end_page | 990 |
| container_issue | 3 |
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| container_title | Genetics (Austin) |
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| creator | Kelkar, Hemant S Griffith, James Case, Mary E Covert, Sarah F Hall, Robert D Keith, Charles H Oliver, J. Steve Orbach, Marc J Sachs, Matthew S Wagner, Jeff R Weise, Michael J Wunderlich, John K Arnold, Jonathan |
| description | A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly |
| doi_str_mv | 10.1093/genetics/157.3.979 |
| format | article |
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Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.</description><identifier>ISSN: 0016-6731</identifier><identifier>ISSN: 1943-2631</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1093/genetics/157.3.979</identifier><identifier>PMID: 11238388</identifier><identifier>CODEN: GENTAE</identifier><language>eng</language><publisher>United States: Genetics Soc America</publisher><subject>Bacteria ; Bacteriophage lambda - genetics ; Chromosome Mapping ; Chromosomes - genetics ; Cloning ; Cosmids - genetics ; Deoxyribonucleic acid ; DNA ; DNA, Complementary - genetics ; DNA, Complementary - metabolism ; Expressed Sequence Tags ; Fungi ; Gene Library ; Genes ; Genetic Linkage ; Genetic Vectors ; Genome, Fungal ; Genomics ; Karyotyping ; Models, Genetic ; Molecular Sequence Data ; Neurospora crassa - genetics ; Nucleic Acid Hybridization ; Phosphotransferases (Alcohol Group Acceptor) - genetics ; Physical Chromosome Mapping ; Sequence Analysis, DNA</subject><ispartof>Genetics (Austin), 2001-03, Vol.157 (3), p.979-990</ispartof><rights>Copyright Genetics Society of America Mar 2001</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c456t-b2ef6dbd68c2b1bc10cdb54f9cec8bc5333f1560a4db478a8dbee343f4a6e78f3</citedby><cites>FETCH-LOGICAL-c456t-b2ef6dbd68c2b1bc10cdb54f9cec8bc5333f1560a4db478a8dbee343f4a6e78f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,777,781,882,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11238388$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kelkar, Hemant S</creatorcontrib><creatorcontrib>Griffith, James</creatorcontrib><creatorcontrib>Case, Mary E</creatorcontrib><creatorcontrib>Covert, Sarah F</creatorcontrib><creatorcontrib>Hall, Robert D</creatorcontrib><creatorcontrib>Keith, Charles H</creatorcontrib><creatorcontrib>Oliver, J. 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Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.</description><subject>Bacteria</subject><subject>Bacteriophage lambda - genetics</subject><subject>Chromosome Mapping</subject><subject>Chromosomes - genetics</subject><subject>Cloning</subject><subject>Cosmids - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Complementary - genetics</subject><subject>DNA, Complementary - metabolism</subject><subject>Expressed Sequence Tags</subject><subject>Fungi</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genetic Linkage</subject><subject>Genetic Vectors</subject><subject>Genome, Fungal</subject><subject>Genomics</subject><subject>Karyotyping</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Data</subject><subject>Neurospora crassa - genetics</subject><subject>Nucleic Acid Hybridization</subject><subject>Phosphotransferases (Alcohol Group Acceptor) - genetics</subject><subject>Physical Chromosome Mapping</subject><subject>Sequence Analysis, DNA</subject><issn>0016-6731</issn><issn>1943-2631</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2001</creationdate><recordtype>article</recordtype><recordid>eNpdkU1v1DAQhi0EokvhD3BAEQdu2XrijzgckKoICtIKDpSzZTuTjaskXuyEVf89Rl1Y4OSDn3k18z6EvAS6Bdqwqz3OuHiXrkDUW7Zt6uYR2UDDWVlJBo_JhlKQpawZXJBnKd1RSmUj1FNyAVAxxZTakPZ2wOIzrjGkQ4imcNGkZIobnMOEb4s2pMl3xc7baKLHVHwNccGusPdFO8QwhZSx5-RJb8aEL07vJfn24f1t-7Hcfbn51F7vSseFXEpbYS8720nlKgvWAXWdFbxvHDplnWCM9SAkNbyzvFZGdRaRcdZzI7FWPbsk7x5yD6udsHM4L9GM-hD9ZOK9Dsbrf39mP-h9-KGBSxCiygFvTgExfF8xLXryyeE4mhnDmnRNpRRAeQZf_wfehTXO-ThdAc_l5WIzVD1ALpeXIvZ_NgGqfwnSvwXpLEgznQXloVd_33AeORk57zj4_XD0EXWazDhmHPTxeDwn_QT-w512</recordid><startdate>20010301</startdate><enddate>20010301</enddate><creator>Kelkar, Hemant S</creator><creator>Griffith, James</creator><creator>Case, Mary E</creator><creator>Covert, Sarah F</creator><creator>Hall, Robert D</creator><creator>Keith, Charles H</creator><creator>Oliver, J. 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The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.</abstract><cop>United States</cop><pub>Genetics Soc America</pub><pmid>11238388</pmid><doi>10.1093/genetics/157.3.979</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0016-6731 |
| ispartof | Genetics (Austin), 2001-03, Vol.157 (3), p.979-990 |
| issn | 0016-6731 1943-2631 1943-2631 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1461552 |
| source | Freely Accessible Science Journals; Alma/SFX Local Collection; Oxford University Press:Jisc Collections:OUP Read and Publish 2024-2025 (2024 collection) (Reading list) |
| subjects | Bacteria Bacteriophage lambda - genetics Chromosome Mapping Chromosomes - genetics Cloning Cosmids - genetics Deoxyribonucleic acid DNA DNA, Complementary - genetics DNA, Complementary - metabolism Expressed Sequence Tags Fungi Gene Library Genes Genetic Linkage Genetic Vectors Genome, Fungal Genomics Karyotyping Models, Genetic Molecular Sequence Data Neurospora crassa - genetics Nucleic Acid Hybridization Phosphotransferases (Alcohol Group Acceptor) - genetics Physical Chromosome Mapping Sequence Analysis, DNA |
| title | The Neurospora crassa Genome: Cosmid Libraries Sorted by Chromosome |
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