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IGMAP: An interactive mapping and clustering platform for plants

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Title IGMAP: An interactive mapping and clustering platform for plants
 
Creator Priya, Piyush
Bandhiwal, Nitesh
Misra, Gopal
Mondal, Subhashish
Yadav, Gitanjali
 
Subject IGMAP
 
Description Accepted date: January 18, 2015
Next-generation sequencing (NGS) technologies have resulted
in a massive surge of high-throughput genomic data, particularly for the plant kingdom, boosting the development of
methods for gene family discovery and identification of clustering patterns at genomic scales. Plants are well known for
the occurrence of both genic and chromosomal duplications
that have resulted in the widespread existence of gene families
in this kingdom, apart from being associated with subsequent
evolutionary divergence via sub-functionalization or neo-
functionalization (Flagel and Wendel, 2009). These divergent
mechanisms eventually lead to the formation of gene clusters,
which in turn, have been shown to confer selective
advantages to the genome including co-inheritance and co-
regulation (Fischbach et al., 2008). Although gene clusters
have been conventionally understood to be the genetic
building blocks of prokaryotic genomes, comparative genomic
studies have revealed the presence of functionally related
genes that are clustered in lower nematodes, fungi, and
several higher eukaryotes (Zorio et al., 1994; Blumenthal,
1998; Lee and Sonnhammer, 2003; Hurst et al., 2004;
Thomas, 2006). However, very few data are available on the
modularity or clustered linkage of genes in plants, despite the
widespread occurrence of duplication events in the kingdom.
In this regard, recent reports of biosynthetic modules and
clustered organization of genes spotted in several major
classes of plant-derived secondary metabolites arising through
neo-functionalization and relocation of duplicated or existing
genes, have offered an exciting niche (Osbourn, 2010). The
presently available approaches for the identification and
analysis of plant gene clusters include map-based cloning, forward and reverse genetics, and genome mining. As the wealth
of plant genome sequence data continues to increase exponentially, newer methods are going to be required to carry out
genome mining in a rational and useful manner.
This work was supported by the BTISNET-grant of Department of
Biotechnology (DBT), Government of India (grant no. BT/BI/04/069/
2006) and the SERB Women’s Excellence Award to G.Y. (grant no. SB/
WEA-014/2013). P.P. was supported by a Senior Research Fellowship
of the Council of Scientific and Industrial Research (CSIR), India.
 
Date 2016-01-21T06:18:34Z
2016-01-21T06:18:34Z
2015
 
Type Article
 
Identifier Mol. Plant, 8(5): 818-821
1674-2052
http://172.16.0.77:8080/jspui/handle/123456789/563
http://www.sciencedirect.com/science/article/pii/S1674205215001057
10.1016/j.molp.2015.01.018
 
Language en_US
 
Publisher Cell Press