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Constructing improved chickpea genome assemblies using skimGBS

OAR@ICRISAT

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Relation http://oar.icrisat.org/10313/
 
Title Constructing improved chickpea genome assemblies using skimGBS
 
Creator Ruperao, P
Bayer, P
Kenneth Chan, C K
Hayashi, S
Roorkiwal, M
Chitikineni, A
Sutton, T
Batley, J
Varshney, R K
Edwards, D
 
Subject Chickpea
Genetics and Genomics
 
Description Chickpea (Cicer arietinum L.) is the second most important grain
legume after soybean and plays an important role in food security.
The application of genomics provides the potential to increase the
productivity and resilience of this important crop. We have developed
a novel strategy to assess and improve the chickpea reference
genomes. The quality of both chickpea desi and kabuli draft
genomes were assessed using sequence data from flow cytometry
isolated chromosomes to identify misplaced contigs. Using
SNPs derived from whole genome sequence data of ICC 4958 x
PI 489777, and skim sequence-based genotyping of this population,
we could validate and correct the draft assembly. In addition
to placing the misplaced sequence regions into corresponding
chromosome positions, most of the previously unplaced contig
sequences have now been incorporated into the pseudomolecules
of the improved version. The total chromosome sequence length
has increased from 124.38 Mb and 347.24 Mb to 375.06 Mb and
423.28 Mb for the desi and kabuli genomes respectively. Both
genomes have been re-annotated. A total of 33,473 genes from
kabuli and 31,419 genes from desi were predicted. Both improved
genomes are available at http://cicer.info.
 
Date 2017-02
 
Type Conference or Workshop Item
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/10313/1/Abstract_Book_418.pdf
Ruperao, P and Bayer, P and Kenneth Chan, C K and Hayashi, S and Roorkiwal, M and Chitikineni, A and Sutton, T and Batley, J and Varshney, R K and Edwards, D (2017) Constructing improved chickpea genome assemblies using skimGBS. In: InterDrought-V, February 21-25, 2017, Hyderabad, India.