Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy

Hoang, Nam V., Furtado, Agnelo, McQualter, Richard B. and Henry, Robert J. (2015) Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy. New Negatives in Plant Science, 1-2 33-45. doi:doi:10.1016/j.neps.2015.10.001

Author Hoang, Nam V.
Furtado, Agnelo
McQualter, Richard B.
Henry, Robert J.
Title Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy
Journal name New Negatives in Plant Science   Check publisher's open access policy
ISSN 2352-0264
Publication date 2015-08-01
Sub-type Article (original research)
DOI doi:10.1016/j.neps.2015.10.001
Open Access Status DOI
Volume 1-2
Start page 33
End page 45
Total pages 13
Place of publication Amsterdam, NX, Netherlands
Publisher Elsevier
Language eng
Formatted abstract
Background:  The chloroplast genome of plants has been frequently sequenced using chloroplast DNA derived by techniques involving chloroplast isolation and or by PCR amplification using primer sequences targeted to amplify the chloroplast genome. Using these approaches, chloroplast heteroplasmy, described as variations in the chloroplast sequence within an individual plant, has been reported in many plant species. More recently, next generation sequencing (NGS) technologies have allowed chloroplast genome sequences to be extracted from shotgun sequences of total plant DNA.

Results:  Here, we used DNA preparations varying in nuclear, mitochondrial and chloroplast enrichment to explore the potential to distinguish genuine chloroplast heteroplasmy from apparent heteroplasmy due to sequence-variant homologues of chloroplast genome sequences inserted in nuclear or mitochondrial genomes. Application of NGS to the whole sugarcane genome followed by read mapping analysis of the complex sugarcane system allowed the assembly of a complete chloroplast genome sequence of sugarcane cv. Q155. Variant analysis showed that they were present only at frequencies that could be attributed to homologues of chloroplast sequences inserted in the nucleus or mitochondria.

Conclusions:  The result suggests that earlier reports of heteroplasmy in chloroplasts may have been due to contaminating sequences from other genomes (nuclear or mitochondrial) in chloroplast preparations or specific amplification of sequences from these genomes. This demonstrates that the ability to evaluate sequence abundance avoids the risks of attributing a chloroplast gene homologue from the nucleus or mitochondria to the chloroplast.
Keyword Chloroplast genome assembly
Chloroplast heteroplasmy
Chloroplast variants
Gene transfer
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2016 Collection
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Created: Thu, 03 Mar 2016, 01:17:05 EST by Annie Morley on behalf of Qld Alliance for Agriculture and Food Innovation