Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses
We constructed and characterized a bacterial artificial chromosome (BAC) library for Epichloë festucae, a genetically tractable fungal plant mutualist. The 6144 clone library with an average insert size of 87kb represents at least 18-fold coverage of the 29 Mb genome. We used the library to assemble...
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| Veröffentlicht in: | Fungal genetics and biology 2004, Vol.41 (1), p.23-32 |
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| container_title | Fungal genetics and biology |
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| creator | Kutil, B.L Liu, G Vrebalov, J Wilkinson, H.H |
| description | We constructed and characterized a bacterial artificial chromosome (BAC) library for Epichloë festucae, a genetically tractable fungal plant mutualist. The 6144 clone library with an average insert size of 87kb represents at least 18-fold coverage of the 29 Mb genome. We used the library to assemble a 110kb contig spanning the putative ornithine decarboxylase (odc) ortholog and subsequently expanded it to 228kb with a single walking step in each direction. Furthermore, we evaluated conservation of microsynteny between E. festucae and some model filamentous fungi by comparing sequence available from a 43kb region at the end of one BAC to publicly available fungal genome sequences. Orthologs to the 13 contiguous open reading frames (ORFs) identified in E. festucae are syntenic in Neurospora crassa and Magnaporthe grisea occurring in small sets of two, three or four colinear ORFs. This library is a valuable resource for research into traits important for the development and maintenance of a plant-fungus mutualistic symbiosis. |
| doi_str_mv | 10.1016/j.fgb.2003.08.004 |
| format | Article |
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This library is a valuable resource for research into traits important for the development and maintenance of a plant-fungus mutualistic symbiosis.</description><subject>Chromosomes, Artificial, Bacterial</subject><subject>Cloning, Molecular</subject><subject>Contig Mapping</subject><subject>Epichloe festucae</subject><subject>Gene Library</subject><subject>Gene Order</subject><subject>Hypocreales - genetics</subject><subject>Magnaporthe - genetics</subject><subject>Magnaporthe grisea</subject><subject>Neurospora crassa</subject><subject>Neurospora crassa - genetics</subject><subject>odc gene</subject><subject>Open Reading Frames</subject><subject>Poaceae - microbiology</subject><subject>Synteny</subject><issn>1087-1845</issn><issn>1096-0937</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkb2O1DAURiMEYn_gAWjAFRUJ13acxCUaLSzSShSwteU41xmPkniwnSKvwtPiaEaipPKVdb5PV_cUxTsKFQXafD5VduwrBsAr6CqA-kVxS0E2JUjevtznri1pV4ub4i7GEwCloqavixtaNzVnorkt_hz8ktxIdIw499NG9DKQ2Zng47YkXPYPPW3RRbJGt2SQ9NokDE5PRIfkrDP7aI7Bzz76Gcnk-qDDRqwP5OHszHHySCzGtBqNn3LBvKZVTy4mZ4hdlzHHcRn8-bglJN6SMezbxDfFK6uniG-v733x_PXh1-GxfPrx7fvhy1NpuGCplKahXOjeDI1k0HLWo0FmrK1BWBSypQy5aQQTbWe0FsYgQNtLM0hRy1by--Ljpfcc_O8176lmFw1Ok17Qr1G1VAjWMf5fkErGWim6DNILuJ8xBrTqHNycb6IoqN2cOqlsTu3mFHQqm8uZ99fytZ9x-Je4qsrAhwtgtVd6DC6q558MKAeQsm6ajv8FX7yiZA</recordid><startdate>2004</startdate><enddate>2004</enddate><creator>Kutil, B.L</creator><creator>Liu, G</creator><creator>Vrebalov, J</creator><creator>Wilkinson, H.H</creator><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>2004</creationdate><title>Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses</title><author>Kutil, B.L ; Liu, G ; Vrebalov, J ; Wilkinson, H.H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c352t-9c6135abcd6920732bece2cff405fe59712e3c652578caa5cce007b9cd9549793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Chromosomes, Artificial, Bacterial</topic><topic>Cloning, Molecular</topic><topic>Contig Mapping</topic><topic>Epichloe festucae</topic><topic>Gene Library</topic><topic>Gene Order</topic><topic>Hypocreales - genetics</topic><topic>Magnaporthe - genetics</topic><topic>Magnaporthe grisea</topic><topic>Neurospora crassa</topic><topic>Neurospora crassa - genetics</topic><topic>odc gene</topic><topic>Open Reading Frames</topic><topic>Poaceae - microbiology</topic><topic>Synteny</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kutil, B.L</creatorcontrib><creatorcontrib>Liu, G</creatorcontrib><creatorcontrib>Vrebalov, J</creatorcontrib><creatorcontrib>Wilkinson, H.H</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Fungal genetics and biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kutil, B.L</au><au>Liu, G</au><au>Vrebalov, J</au><au>Wilkinson, H.H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses</atitle><jtitle>Fungal genetics and biology</jtitle><addtitle>Fungal Genet Biol</addtitle><date>2004</date><risdate>2004</risdate><volume>41</volume><issue>1</issue><spage>23</spage><epage>32</epage><pages>23-32</pages><issn>1087-1845</issn><eissn>1096-0937</eissn><abstract>We constructed and characterized a bacterial artificial chromosome (BAC) library for Epichloë festucae, a genetically tractable fungal plant mutualist. The 6144 clone library with an average insert size of 87kb represents at least 18-fold coverage of the 29 Mb genome. We used the library to assemble a 110kb contig spanning the putative ornithine decarboxylase (odc) ortholog and subsequently expanded it to 228kb with a single walking step in each direction. Furthermore, we evaluated conservation of microsynteny between E. festucae and some model filamentous fungi by comparing sequence available from a 43kb region at the end of one BAC to publicly available fungal genome sequences. Orthologs to the 13 contiguous open reading frames (ORFs) identified in E. festucae are syntenic in Neurospora crassa and Magnaporthe grisea occurring in small sets of two, three or four colinear ORFs. 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| ispartof | Fungal genetics and biology, 2004, Vol.41 (1), p.23-32 |
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| language | eng |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Chromosomes, Artificial, Bacterial Cloning, Molecular Contig Mapping Epichloe festucae Gene Library Gene Order Hypocreales - genetics Magnaporthe - genetics Magnaporthe grisea Neurospora crassa Neurospora crassa - genetics odc gene Open Reading Frames Poaceae - microbiology Synteny |
| title | Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloe festucae, a mutualistic fungal endophyte of grasses |
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