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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF PEST RESISTANCE AND QUALITY TRAITS OF SOYBEAN

Location: Corn, Soybean and Wheat Quality Research Unit

Title: Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

Authors
item Bai, Xiaodong -
item Wei, Zhang -
item Orantes, Lucia -
item Jun, Tae-Hwan -
item Mittapalli, O -
item Mian, Rouf
item Michel, Andrew -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 25, 2010
Publication Date: June 29, 2010
Repository URL: http://hdl.handle.net/10113/45258
Citation: Bai, X., Wei, Z., Orantes, L., Jun, T., Mittapalli, O., Mian, R.M., Michel, A.P. 2010. Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines. PLoS One. 5(6): e11370. doi:10.1371/journal.pone.0011370.

Interpretive Summary: Soybean aphid has become the most important insect pest of soybean in North America. Recent genetic and genomic research has developed molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, soybean aphid, Aphis glycines, has no significant molecular resources. Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to rapidly develop a large number of molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 expressed sequence tags and 56,688 genomic contigs. From this data set, 598 single nucleotide polymorphism and 1,395 microsatellite makers were identified. In addition, we uncovered 39,822 bp of sequences related to the primary endosymbiont, Buchnera aphidicola, as well as sequences from various secondary endosymbionts. Endosymbionts are bacteria that live inside the gut of aphids and help aphids digest their meals. The power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and provide better tools for controlling the soybean aphid.

Technical Abstract: Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources. Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to rapidly characterize the transcriptome and to generate a large number of molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 ESTS and 56,688 genomic contigs. From this data set, 598 SNPs and 1,395 microsatellite makers were identified. In addition, we uncovered 39,822 bp of sequences related to the primary endosymbiont, Buchnera aphidicola, as well as sequences from various secondary endosymbionts. Molecular resources for an invasive, non-model aphid species were rapidly expanded. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and provide novel targets for soybean aphid control.

Last Modified: 9/1/2014
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