Genomic organization of the fungus Phycomyces |
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| Institution: | 1. National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China;1. Dipartimento di Ingegneria Civile, Ambientale, Aerospaziale, dei Materiali, Università di Palermo, Viale delle Scienze, Ed. 8, Palermo (IT), Italy;2. Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA;3. Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK;4. Waterways d.o.o., Gornji Vukojevac 10A, 44272 Lekenik, Croatia;5. School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia;6. University of Innsbruck, Unit for Environmental Engineering, Technikerstrasse 13, 6020 Innsbruck, Austria;7. Department of Environmental Engineering, Technical University of Denmark (DTU Environment), Miljøvej B115, Kgs. Lyngby, 2800, Denmark;8. The University of Queensland Advanced Water Management Centre (AWMC), QLD 4072, Australia;9. KU Leuven, Dept. of Civil Engineering, Hydraulics Section Kasteelpark Arenberg 40, Box 2448, 3001 Leuven, Belgium;1. Hertie Institute for Clinical Brain Research, Department of Neurodegenerative diseases, University of Tübingen, Tübingen, Germany;2. German Center for Neurodegenerative diseases (DZNE), Tübingen, Germany |
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| Abstract: | The fungus Phycomyces blakesleeanus has a relatively small genome, 30 megabases (Mb), with a low guanine and cytosine (G+C) content, 35%; the coding sequences cloned to date all have a G+C content of about 50%. In order to investigate the organization of the genome of this fungus, we have cloned and sequenced 251 DNA fragments. One hundred and twenty-six clones were obtained by digestion with MspI (target sequence 5′-CCGG-3′) and 125 random clones were obtained by sonication. The average length of sequence obtained was about 200 base pairs (bp) and the total length was about 50 kilobases (kb). The G + C content is not homogeneous throughout the genome: sequences obtained after digestion with MspI have an average of 5% more G + C content than the random fragments, and are enriched in coding sequences. Fourteen MspI fragments show similarities to known proteins and 21 encode ribosomal RNA (rRNA). By contrast, only three of the random fragments are similar to known proteins and only one to a rRNA. We conclude that the Phycomyces genome is composed of G+C-rich genes surrounded by G+C-poor areas. Two clones have similarities to the transposase of the transposon Tcl from Caenorhabditis elegans. This result suggests the presence of a high copy number of a Tcl-like transposable element in the Phycomyces genome. Another clone was similar to the transposon Txl from Xenopus laevis. A novel repetitive nt sequence has been characterized; about 5% of the total genome is a repetition of any of two consensus sequences of 31 by named PrAI and PrA2. |
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