The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

Abstract

Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut. A r t i c l e s npg © 2016 Nature America, Inc. All rights reserved.Nature GeNetics VOLUME 48 | NUMBER 4 | APRIL 2016 4 3 9 subgenomes of A. hypogaea. Progeny are vigorous, phenotypically normal and fertile and showed lower segregation distortion 16,17 than has been observed for some populations derived from A. hypogaea intraspecific crosses [18][19][20][21] . Therefore, as a first step to characterizing the genome of cultivated peanut, we sequenced and analyzed the genomes of the two diploid ancestors of cultivated peanut. RESULTS Sequencing and assembly of the diploid A and B genomesConsidering that A. duranensis V14167 and A. ipaensis K30076 are likely good representatives of the ancestral species of A. hypogaea, we sequenced their genomes. After filtering, the data generated from the seven paired-end libraries corresponded to an estimated 154× and 163× base-pair coverage for A. duranensis and A. ipaensis, respectively (Supplementary Tables 1-6). The total assembly sizes were 1,211 and 1,512 Mb for A. duranensis and A. ipaensis, respectively, of which 1,081 and 1,371 Mb were represented in scaffolds of 10 kb or greater in size (Supplementary Table 7). Ultradense genetic maps were generated through genotyping by sequencing (GBS) of two diploid recombinant inbred line (RIL) populations (Supplementary Data Set 1). SNPs within scaffolds were used to validate the assemblies and confirmed their high quality; 190 of 1,297 initial scaffolds of A. duranensis and 49 of 353 initial scaffolds of A. ipaensis were identified as chimeric, on the basis of the presence of diagnostic population-wide switches in genotype calls occurring at the point of misjoin. Chimeric scaffolds were split, and their components were remapped. Thus, approximate chromosomal placements were obtained for 1,692 and 459 genetically verified scaffolds, respectively. Conventional molecular marker maps (Supplementary Data Set 2) and syntenic inferences were then used to refine the ordering of scaffolds within the initial genetic bins. Generally, agreement was good for maps in euchromatic arms and poorer in pericentromeric regions (although one map 22 showed large inversions in two lin...

Research Article Coupled transcript and metabolite identification: insights on induction and synthesis of resveratrol in peanut, wild relatives and synthetic allotetraploid.

“…The amplification in all samples using primers designed using sequences from two different species suggested that RS gene family originated before speciation, at least in section Arachis that comprises the samples analyzed. RS gene family has not been studied in wild Arachis, but evidences show peanuts and their wild relatives have many similarities on gene content (Bertioli et al, 2016). Thus, we assume wild Arachis also have a RS gene family.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Genome sequences for most of the grain legumes are now available, for instance soybean (Schmutz et al, 2010), groundnut progenitors (Bertioli et al, 2016;Chen et al, 2016), chickpea (Varshney et al, 2013d;Parween et al, 2015), pigeonpea (Varshney et al, 2012a), common bean (Schmutz et al, 2014;Yang et al, 2015), and adzuki bean (Kang et al, 2015;Yang et al, 2015) (Table 1). Efforts are underway to sequence the remaining legume genomes.…”

Stress Responses of Peanut (<i>Arachis hypogaea</i> L.) Genotypes as Measured by Trigonelline Content after Exposure to UV-B Radiation

“…It is not likely that one genotype would be significantly better adapted for UV-B rich environments or preferable for UV-B induced trigonelline biosynthesis over any other genotype. This may be due in part to low levels of genetic polymorphism (2.8% on average) between peanut genotypes and similarities with ancestral species [36]. However, trigonelline concentrations increased in all genotypes after irradiation by UV-B.…”