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Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Prentis, Peter, Woolfit, Megan, Thomas-Hall, Skye, Ortiz-Barrientos, Daniel, Pavasovic, Ana, Lowe, Andrew, & Schenk, Peer (2010) Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Annals of Botany, 106(6), pp. 1009-1017.

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Abstract

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species.

Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies.

Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens.

Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

Impact and interest:

17 citations in Scopus
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14 citations in Web of Science®

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ID Code: 45082
Item Type: Journal Article
Additional Information: Articles free to read on journal website after 12 months
Keywords: ESTs, genomics, invasive species, maternal effects, rapid adaptation, selection, Senecio madagascariensis
DOI: 10.1093/aob/mcq201
ISSN: 0305-7364
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > PLANT BIOLOGY (060700)
Deposited On: 24 Aug 2011 22:16
Last Modified: 22 Jan 2015 05:28

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