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      Draft Genome Sequence of Salmacisia buchloëana (Basidiomycota), Which Induces Hermaphroditism in Dioecious Buffalograss

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          ABSTRACT

          Here, we report the draft genome of Salmacisia buchloëana type strain OK1, a monotypic species of fungi that induces ovary development in genetic male plants and increases reproductive biomass allocation in its host buffalograss. This research will enhance our understanding of fungal manipulation of host development at the genomic level.

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          Plant infection and the establishment of fungal biotrophy.

          Kurt Mendgen, Matthias Hahn (2002)
          To exploit plants as living substrates, biotrophic fungi have evolved remarkable variations of their tubular cells, the hyphae. They form infection structures such as appressoria, penetration hyphae and infection hyphae to invade the plant with minimal damage to host cells. To establish compatibility with the host, controlled secretory activity and distinct interface layers appear to be essential. Colletotrichum species switch from initial biotrophic to necrotrophic growth and are amenable to mutant analysis and molecular studies. Obligate biotrophic rust fungi can form the most specialized hypha: the haustorium. Gene expression and immunocytological studies with rust fungi support the idea that the haustorium is a transfer apparatus for the long-term absorption of host nutrients.
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            A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.

            Colette Breuill, Joerg Bohlmann, Tom Hsiang … (2011)
            We offer a guide to de novo genome assembly using sequence data generated by the Illumina platform for biologists working with fungi or other organisms whose genomes are less than 100Mb in size. The guide requires no familiarity with sequencing assembly technology or associated computer programs. It defines commonly used terms in genome sequencing and assembly; provides examples of assembling short-read genome sequence data for four strains of the fungus Grosmannia clavigera using four assembly programs; gives examples of protocols and software; and presents a commented flowchart that extends from DNA preparation for submission to a sequencing center, through to processing and assembly of the raw sequence reads using freely available operating systems and software. Copyright © 2011 Elsevier B.V. All rights reserved.
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              Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis.

              Yi Li, Tom Hsiang, Rui-Heng Yang … (2016)
              Ophiocordyceps sinensis is one of the most expensive medicinal fungi world-wide, and has been used as a traditional Chinese medicine for centuries. In a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of Roche 454 (223Mb) and Illumina HiSeq (10.6Gb) sequencing data, producing a genome of 87.7Mb with an N50 scaffold length of 12kb and 6972 predicted genes. To test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic DNA extractions of a single ascospore isolate (strain 1229) on an Illumina HiSeq platform (25Gb total data). Assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (ABySS, SOAP and Velvet). In nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher N50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher N50 values. Depending on the assembly program and data type, the maximal N50 was reached with between 50% to 90% of the total read data, equivalent to 100× to 200× coverage. The draft genome assembly was improved over the previously published version resulting in a 114Mb assembly, scaffold N50 of 70kb and 9610 predicted genes. Among the predicted genes, 9213 were validated by RNA-Seq analysis in this study, of which 8896 were found to be singletons. Evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100× and 200×.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 6 April 2017
                Publication date Collection: April 2017
                Volume: 5
                Issue: 14
                Electronic Location Identifier: e00142-17
                Affiliations
                [a ]Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, USA
                [b ]School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
                [c ]Texas A&M AgriLife Research and Extension Center, Dallas, Texas, USA
                [d ]Intercollege Graduate Degree Program in Plant Biology, Huck Institute of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
                Author notes
                Address correspondence to David R. Huff, drh15@ 123456psu.edu .
                Article
                Publisher ID: genomeA00142-17
                DOI: 10.1128/genomeA.00142-17
                PMC ID: 5383901
                PubMed ID: 28385853
                SO-VID: 5514a381-4b30-4144-9062-06c73c694b41
                Copyright © Copyright © 2017 Huff et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 7 February 2017
                Date accepted : 10 February 2017
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 10, Pages: 2, Words: 1099
                Funding
                Funded by: Huck Institute of Life Sciences, Penn State University
                Award Recipient : David Robert Huff
                Funded by: Pennsylvania Turfgrass Council
                Award Recipient : David Robert Huff
                Funded by: NIFA Hatch Project
                Award ID: 1006804
                Award Recipient : David Robert Huff
                Categories
                Subject: Eukaryotes
                Custom metadata
                cover-date April 2017

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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