An efficient approach to BAC based assembly of complex genomes

Visendi, Paul, Berkman, Paul J., Hayashi, Satomi, Golicz, Agnieszka A., Bayer, Philipp E., Ruperao, Pradeep, Hurgobin, Bhavna, Montenegro, Juan, Chan, Chon-Kit Kenneth, Stankova, Helena, Batley, Jacqueline, Simkova, Hana, Dolezel, Jaroslav and Edwards, David (2016) An efficient approach to BAC based assembly of complex genomes. Plant Methods, 12 1: . doi:10.1186/s13007-016-0107-9


Author Visendi, Paul
Berkman, Paul J.
Hayashi, Satomi
Golicz, Agnieszka A.
Bayer, Philipp E.
Ruperao, Pradeep
Hurgobin, Bhavna
Montenegro, Juan
Chan, Chon-Kit Kenneth
Stankova, Helena
Batley, Jacqueline
Simkova, Hana
Dolezel, Jaroslav
Edwards, David
Title An efficient approach to BAC based assembly of complex genomes
Journal name Plant Methods   Check publisher's open access policy
ISSN 1746-4811
Publication date 2016-01-20
Sub-type Article (original research)
DOI 10.1186/s13007-016-0107-9
Open Access Status DOI
Volume 12
Issue 1
Total pages 9
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2017
Language eng
Formatted abstract
Background
There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate ‘gold’ reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success.

Results
We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes.

Conclusion
s
We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.
Keyword 7DS
Assembly
BAC
Next-generation sequencing
Saccharum spp
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ
Additional Notes Article number 2

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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