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De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Overview of attention for article published in BMC Genomics, March 2016
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  • Above-average Attention Score compared to outputs of the same age (58th percentile)

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Citations

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65 Mendeley
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Title
De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways
Published in
BMC Genomics, March 2016
DOI 10.1186/s12864-016-2599-0
Pubmed ID
Authors

Shailaja Hittalmani, H. B. Mahesh, Channappa Mahadevaiah, Mothukapalli Krishnareddy Prasannakumar

Abstract

Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth. The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future. Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 65 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
India 1 2%
Unknown 64 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 18 28%
Student > Ph. D. Student 13 20%
Student > Master 9 14%
Student > Doctoral Student 6 9%
Student > Postgraduate 3 5%
Other 9 14%
Unknown 7 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 33 51%
Biochemistry, Genetics and Molecular Biology 15 23%
Environmental Science 2 3%
Computer Science 1 2%
Arts and Humanities 1 2%
Other 4 6%
Unknown 9 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 June 2021.
All research outputs
#10,269,081
of 18,925,022 outputs
Outputs from BMC Genomics
#3,926
of 9,662 outputs
Outputs of similar age
#112,612
of 273,393 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 18,925,022 research outputs across all sources so far. This one is in the 45th percentile – i.e., 45% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,662 research outputs from this source. They receive a mean Attention Score of 4.5. This one has gotten more attention than average, scoring higher than 58% of its peers.
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We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them