Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection

Abstract

BackgroundCultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.ResultsTranscriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.ConclusionsThis study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

“…Since the generated reads can assemble without a reference genome, it is also an ideal tool for transcriptome sequencing for those species without a sequenced genome [17]. Recently, RNA-Seq has been used to analyze the transcriptomic profiles of oil accumulation in oil plants such as Jatropha ( Jatropha curcas ) [18], oil tea ( Camellia oleifera ) [19], oil palm ( Elaeis guineensis ) [20], peanut ( Arachis hypogaea ) [21], rapeseed ( Brassica napus ) [22], and sesame ( Sesamum indicum ) [23]. However, the functional genes involved in the oil biosynthesis and metabolism of S. paniculata are not yet to be investigated.…”

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

“…Advances in other marker types, such as randomly amplified polymorphic DNA (RAPD) (Halward and Stalker, 1991;Halward et al, 1992), restriction fragment length polymorphism (RFLP) (Halward and Stalker, 1991;Kochert et al, 1996;Burow et al, 2009), amplified fragment length polymorphism (AFLP) (Herselman et al, 2004), simple sequence repeat (SSR) (He et al, 2003;Gimenes et al, 2007;Cuc et al, 2008;Liang et al, 2009), sequence-related amplified polymorphism (SRAP) , single strand conformational polymorphism (SSCP) (Nagy et al, 2010), and single nucleotide polymorphism (SNP) (Nagy et al, 2012), soon replaced the early exploration with proteins. During the past two decades, much effort has been made to develop genetic and genomic tools in cultivated peanut, such as construction of BAC libraries (Yuksel and Paterson, 2005;Guimarães et al, 2008), cDNA libraries (Luo et al, 2005;Proite et al, 2007;Guo et al, 2008Guo et al, , 2009Koilkonda et al, 2012), RNAseq using next generation sequencing technology (Guimaraes et al, 2012;Zhang et al, 2012) and development of DNA markers (see reviews of Feng et al, 2012;Pandey et al, 2012;Zhao et al, 2012; (Table 1). Among the various molecular markers investigated to date, simple sequence repeats (SSR) have emerged as one of the preferred DNA marker system for conducting genetic and genomic studies in cultivated peanut.…”

“…Although it is still a challenge to assemble whole complex genome using NGS, the technology has facilitated cost-effective, large scale generation of ESTs. Since the reports of Pandey et al (2012) and Zhao et al (2012), there have been two publications of using NGS to generate EST-SSRs Guimaraes et al, 2012) (Table 1) and for SNP development (Nagy et al, 2012). Zhang et al (2012) …”

“…In addition, 3919 microsatellite markers were developed from the unigene library, and 160 PCR primers for SSR loci were used for validation. Guimaraes et al (2012) used 454 GS FLX Titanium to generate a total of 7.4 3 10 5 raw sequence reads covering 211 Mbp of two A-genome species (A. stenosperma and A. duranensis). High quality reads were assembled to 7723 contigs for A. stenosperma and 12,792 for A. duranensis.…”

Prediction of Leymus arenarius (L.) antimicrobial peptides based on de novo transcriptome assembly

“…It allows discovering new genes, obtaining RNA expression patterns and detecting low-abundance transcripts. Using NGS technology a number of non-model plant transcriptomes and their resistance genes have been analyzed (Guimaraes et al 2012;Prasath et al 2014;Sun et al 2013;Zhao et al 2012). Obviously, an analysis of lymegrass transcriptome will lead to revealing novel components of plant immunity that contribute to the development of wild plant genetics.…”