1
|
Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A 2006; 103:15200-5. [PMID: 17015832 PMCID: PMC1622800 DOI: 10.1073/pnas.0607335103] [Citation(s) in RCA: 359] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.
Collapse
Affiliation(s)
- B. S. Goldman
- *Monsanto Company, St. Louis, MO 63167
- To whom correspondence may be addressed. E-mail:
| | - W. C. Nierman
- The Institute for Genomic Research, Rockville, MD 20850
- Department of Biochemistry and Molecular Biology, George Washington University, Washington, DC 20052
| | - D. Kaiser
- Departments of Biochemistry and Developmental Biology, Stanford University, Stanford, CA 94305
- To whom correspondence may be addressed at:
Department of Developmental Biology, B300 Beckman Center, 279 Campus Drive, Stanford, CA 94305. E-mail:
| | - S. C. Slater
- *Monsanto Company, St. Louis, MO 63167
- **Biodesign Institute, Arizona State University, Tempe, AZ 85287-5001; and
| | - A. S. Durkin
- The Institute for Genomic Research, Rockville, MD 20850
| | - J. A. Eisen
- The Institute for Genomic Research, Rockville, MD 20850
| | - C. M. Ronning
- The Institute for Genomic Research, Rockville, MD 20850
| | | | | | - C. Field
- *Monsanto Company, St. Louis, MO 63167
| | | | - G. Hinkle
- *Monsanto Company, St. Louis, MO 63167
| | | | - H. S. Kim
- The Institute for Genomic Research, Rockville, MD 20850
| | - C. Mackenzie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030
| | - R. Madupu
- The Institute for Genomic Research, Rockville, MD 20850
| | - N. Miller
- *Monsanto Company, St. Louis, MO 63167
| | | | | | - M. Vaudin
- *Monsanto Company, St. Louis, MO 63167
| | | | - H. B. Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030
| |
Collapse
|
2
|
Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA, Feldblyum T, Nierman WC, Fraser CM. Mouse BAC ends quality assessment and sequence analyses. Genome Res 2001; 11:1736-45. [PMID: 11591651 PMCID: PMC311142 DOI: 10.1101/gr.179201] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing success rate of >80%, an average read length of 485 bp, and ABI3700 capillary sequencers, we have generated 449,234 nonredundant mouse BAC end sequences (mBESs) with 218 Mb total from 257,318 clones from libraries RPCI-23 and RPCI-24, representing 15x clone coverage, 7% sequence coverage, and a marker every 7 kb across the genome. A total of 191,916 BACs have sequences from both ends providing 12x genome coverage. The average Q20 length is 406 bp and 84% of the bases have phred quality scores > or = 20. RPCI-24 mBESs have more Q20 bases and longer reads on average than RPCI-23 sequences. ABI3700 sequencers and the sample tracking system ensure that > 95% of mBESs are associated with the right clone identifiers. We have found that a significant fraction of mBESs contains L1 repeats and approximately 48% of the clones have both ends with > or = 100 bp contiguous unique Q20 bases. About 3% mBESs match ESTs and > 70% of matches were conserved between the mouse and the human or the rat. Approximately 0.1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community.
Collapse
Affiliation(s)
- S Zhao
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|