Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.—the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

Abstract

We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.

Potential Functional Replacement of the Plastidic Acetyl-CoA Carboxylase Subunit (accD) Gene by Recent Transfers to the Nucleus in Some Angiosperm Lineages

“…Plastome sequencing studies have revealed that ptaccD is present in three Asteraceae species (G. abyssinica, H. annuus, and L. sativa) but absent in T. caeruleum (Campanulaceae) plastome due to DNA rearrangements (Timme et al, 2007;Haberle et al, 2008;Dempewolf et al, 2010). To estimate more precisely the evolutionary timing of the loss of this pt-accD gene, slot-blot hybridization of total cellular DNA was undertaken from 18 Asterales species (Fig.…”

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

“…Although extensive studies have reported the comparative chloroplast genome analysis in many families (Wu et al 2011;Ghimiray and Sharma 2014), a systematic analysis of the structure and organization of chloroplast genomes in Asteraceae family has not been performed up to now. Here, eight chloroplast genomes belonging to different tribes of Asteraceae family are selected as the representative to perform comparative analysis, including Ageratina adenophora (NC_015621) belonging to the tribe Eupatorieae (Nie et al 2012), Artemisia frigida (NC_020607) (Liu et al 2013), Chrysanthemum indicum (NC_020320), and Chrysanthemum × morifolium (NC_020092) all belonging to the tribe Anthemideae, Guizotia abyssinica (NC_010601) (Dempewolf et al 2010) belonging to the tribe Millerieae, Helianthus annuus (NC_007977) (Timme et al 2007) belonging to the tribe Heliantheae and Jacobaea vulgaris (NC_015543) (Doorduin et al 2011) belonging to the Senecioneae clade as well as Lactuca sativa (DQ383816) (Timme et al 2007) belonging to the tribe Lactucinae, with the purpose to compare and analyze the gene content, genome structure, and RNA editing of Asteraceae cp genomes, which will provide helpful information for better understanding of cp genome evolution within this family.…”

Next-generation hybridization and introgression

“…These include cDNA sequences from transcriptomes, complete organelle genomes and even complete nuclear genomes (Dempewolf et al, 2010;Stapley et al, 2010). These large-scale genomic resources typically allow us to identify many hundreds of SSRs and tens of thousands of SNPs within species.…”

“…Software to identify the most variable gene regions have been developed (for example, BMGE; Criscuolo and Gribaldo, 2010), and once located cloning or bioinformatic analyses can be used to ensure single copies are present, and PCR-optimized to ensure consistent amplification of a range of species. The completion of a suite of genetic and genomic resources for the asterid Guizotia abyssinica (Dempewolf et al, 2010) illustrates the possible outputs from NGS data, which can be used for marker design.…”

“…Ideally, these studies aim to have a good coverage of markers distributed across the genome, with a high marker density, in order to accurately detect introgressed linkage blocks. However, this idealized situation is far from reality in all but the most well-developed model systems (Rieseberg et al, 2000;Dempewolf et al, 2010). A major limitation when assessing introgression is the availability of genetic resources to accurately estimate interspecific gene flow; where insufficient molecular markers or gene sequences are studied, cryptic introgression is likely to go undetected (Currat et al, 2008).…”