Improved Draft Genome Sequence of a Monoteliosporic Culture of the Karnal Bunt ( Tilletia indica ) Pathogen of Wheat

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ABSTRACT

Karnal bunt of wheat is an internationally quarantined fungal pathogen disease caused by Tilletia indica and affects the international commercial seed trade of wheat. We announce here the first improved draft genome assembly of a monoteliosporic culture of the Tilletia indica fungus, consisting of 787 scaffolds with an approximate total genome size of 31.83 Mbp, which is more accurate and near to complete than the previous version.

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Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

T Thiel, W Michalek, R. K. Varshney … (2003)

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

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Toward almost closed genomes with GapFiller

Marten Boetzer, Walter Pirovano (2012)

De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.

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Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern … (2006)

Background In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence. Results We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. Our method is only moderately effected by the length of a database match. Further, it exploits the information that can be derived from the absence of such matches. As a special case, AUGUSTUS+ can predict genes under user-defined constraints, e.g. if the positions of certain exons are known. With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly. Conclusion Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. When a match of a sequence interval to an EST or protein sequence is used it should be treated as compound information rather than as information about individual positions.

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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): 17 May 2018

Publication date Collection: May 2018

Volume: 6

Issue: 20

Electronic Location Identifier: e00015-18

Affiliations

[a ]Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India

[b ]ICAR-Agricultural Knowledge Management Unit, Indian Agricultural Research Institute, Pusa Campus, New Delhi, India

[c ]Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India

[d ]Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, Tallinn, Estonia

[e ]Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India

[f ]Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India

Author notes

Address correspondence to Anil Kumar, anilkumar.mbge@ 123456gmail.com , or Soma S. Marla, ssmarl@ 123456yahoo.com .

A.K., P.M., R.M., and S.S.M. contributed equally to this work.

Author information

Anil Kumar https://orcid.org/0000-0002-9558-4779

Pallavi Mishra https://orcid.org/0000-0001-6789-2179

Ranjeet Maurya https://orcid.org/0000-0002-0306-8970

Article

Publisher ID: genomeA00015-18

DOI: 10.1128/genomeA.00015-18

PMC ID: 5958260

PubMed ID: 29773612

SO-VID: f73c58f0-d95e-4cb8-9862-0845dde3e00a

License:

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

History

Date received : 7 January 2018

Date accepted : 20 March 2018

Page count

Figures: 0, Tables: 0, Equations: 0, References: 23, Pages: 3, Words: 1608

Funding

Funded by: Department of Biotechnology, Ministry of Science and Technology (DBT), https://doi.org/10.13039/501100001407;

Award ID: BT/PR14987/AGR/21/914/2015

Award Recipient : Anil Kumar

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cover-date May 2018

ScienceOpen disciplines: Genetics

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ScienceOpen disciplines: Genetics

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Improved Draft Genome Sequence of a Monoteliosporic Culture of the Karnal Bunt (Tilletia indica) Pathogen of Wheat

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Most cited references 8

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

Toward almost closed genomes with GapFiller

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

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