NDLI: Wheat Zapper: a flexible online tool for colinearity studies in grass genomes

Content Provider	Springer Nature Link
Author	Alnemer, Loai M. Seetan, Raed I. Bassi, Filippo M. Chitraranjan, Charith Helsene, Adam Loree, Paul Goshn, Steve Bou Gu, Yong Q. Luo, Ming Cheng Iqbal, M. Javed Lazo, Gerard R. Denton, Anne M. Kianian, Shahryar F.
Copyright Year	2013
Abstract	In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The “Wheat Zapper” application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the “Wheat Zapper” prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of “Wheat Zapper” was calculated at 0.65 considering the “Genome Zipper” application as the “gold” standard. The differences between these two tools are amply discussed, making the point that “Wheat Zapper” is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/ .
Starting Page	11
Ending Page	17
Page Count	7
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	13
Issue Number	1
e-ISSN	14387948
Language	English
Publisher	Springer-Verlag
Publisher Date	2013-03-10
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Synteny Fine mapping Microsynteny Rice Sorghum Brachypodium Cell Biology Plant Genetics & Genomics Microbial Genetics and Genomics Biochemistry Bioinformatics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q

The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice

Targeted mapping of ESTs linked to the adult plant resistance gene Lr46 in wheat using synteny with rice

A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes

Macro- and microcolinearity between the genomic region of wheat chromosome 5B containing the Tsn1 gene and the rice genome

Control of flowering time and spike development in cereals: the earliness per se Eps-1 region in wheat, rice, and Brachypodium

The PDI genes of wheat and their syntenic relationship to the esp2 locus of rice

Wheat Zapper: a flexible online tool for colinearity studies in grass genomes

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Wheat Zapper: a flexible online tool for colinearity studies in grass genomes