Title |
Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
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Published in |
BMC Genomics, November 2017
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DOI | 10.1186/s12864-017-4243-z |
Pubmed ID | |
Authors |
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Antonio G. Pisabarro, Lucía Ramírez |
Abstract |
Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species. |
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Geographical breakdown
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Spain | 3 | 27% |
France | 1 | 9% |
Taiwan | 1 | 9% |
Unknown | 6 | 55% |
Demographic breakdown
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Scientists | 8 | 73% |
Members of the public | 3 | 27% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 40 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 9 | 23% |
Researcher | 7 | 18% |
Student > Master | 5 | 13% |
Student > Postgraduate | 3 | 8% |
Student > Bachelor | 2 | 5% |
Other | 5 | 13% |
Unknown | 9 | 23% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 16 | 40% |
Biochemistry, Genetics and Molecular Biology | 4 | 10% |
Environmental Science | 3 | 8% |
Chemical Engineering | 2 | 5% |
Business, Management and Accounting | 1 | 3% |
Other | 3 | 8% |
Unknown | 11 | 28% |