Chromosomal and phylogenetic context for conglutin genes in Arachis based on genomic sequence

Ramos, María Laura; Fleming, G. H.; Chu, Ye; Akiyama, Yukio; Gallo, Maria; Ozias‐Akins, Peggy

doi:10.1007/s00438-006-0114-z

Cited by 61 publications

(53 citation statements)

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“…13), makes the assembly of the peanut genome sequence very challenging. However, the A and B subgenomes appear to have undergone relatively few changes since polyploidization: genomic in situ hybridization (GISH), using genomic DNA from the diploid species as probes, clearly distinguishes A and B chromosomes and does not show large A-B mosaics 7,8 . Also, the genome size of A. hypogaea is close to the sum of those for A. duranensis and A. ipaensis (1.25 and 1.56 Gb, respectively 14 ), indicating that there has been no large change in genome size since polyploidy.…”

Section: Openmentioning

confidence: 99%

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

et al. 2016

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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...

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Section: Openmentioning

confidence: 99%

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

et al. 2016

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“…These additional 12 amino acids in Ara h 2.02 corresponded to the difference in molecular mass of the two Ara h 2 bands found on SDS-PAGE (Chatel et al, 2003). Recently, it was shown that these isoforms are homeologous genes that are orthologs, each derived from one of the diploid ancestors of peanut (Ramos et al, 2006).…”

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confidence: 91%

Temporal and Spatial Expression of the Major Allergens in Developing and Germinating Peanut Seed

et al. 2007

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Peanut (Arachis hypogaea) seed proteins Ara h 1, Ara h 2, and Ara h 3 are considered to be the major peanut allergens. However, little is known about their temporal and spatial expression during seed development and upon germination and seedling growth. In this study, transcript levels of the three major peanut allergen genes, ara h 1, ara h 2, and ara h 3, and their corresponding proteins were found in all cultivars. Expression patterns were heterogeneous depending on the specific peanut allergen gene and the cultivars tested. However, ara h 3 expression patterns among the cultivars were more variable than ara h 1 and ara h 2. Transcripts were tissue specific, observed in seeds, but not in leaves, flowers, or roots, and were undetectable during seed germination. In situ hybridizations and immunotissue prints revealed that both embryonic axes and cotyledons expressed the allergens. However, more ara h 1 and ara h 3 messenger RNA was detected in cotyledons relative to embryonic axes. Allergen polypeptide degradation patterns were different in embryonic axes compared with cotyledons during germination and seedling growth, with levels of Ara h 1 and Ara h 2 dramatically reduced compared to the Ara h 3 polypeptides in embryonic axes. These characterization studies of major peanut allergen genes and their corresponding seed storage proteins can provide the basic information needed for biochemical and molecular approaches to obtain a hypoallergenic peanut.

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“…Because of the extent and seriousness of hypersensitive reactions, these allergens and associated genes are being intensely studied to identify specific epitopes, to develop detection methods in foods, and to develop strategies to reduce hypersensitivity to peanut [45]. Research to reduce peanut allergenicity by manipulation of the peanut genome is in progress [43].…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Peanut Seed Storage Proteins and Genetic Variation in a Potential Peanut Allergen

Guo¹,

Liang²,

Chung³

et al. 2008

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Peanut allergy is one of the most severe food allergies. One effort to alleviate this problem is to identify peanut germplasm with lower levels of allergens which could be used in conventional breeding to produce a less allergenic peanut cultivar. In this study, we identified one peanut line, GT-C9, lacking several seed proteins, which were identified as Ara h 3 isoforms by peptide sequencing and named iso-Ara h 3. Total seed proteins were analyzed by one-dimensional (SDS-PAGE) and two-dimensional gel electrophoreses (2-D PAGE). The total protein extracts were also tested for levels of protein-bound end products or adducts such as advanced glycation end products (AGE) and N-(carboxymethyl) lysine (CML), and IgE binding. Peanut genotypes of GT-C9 and GT-C20 exhibited significantly lower levels of AGE adducts and of IgE binding. This potential peanut allergen iso-Ara h 3 was confirmed by peptide sequences and Western blot analysis using specific anti-Ara h 1, Ara h 2, and Ara h 3 antibodies. A full-length sequence of iso-ara h 3 (GenBank number DQ855115) was obtained. The deduced amino acid sequence iso-Ara h 3 (ABI17154) has the first three of four IgE-binding epitopes of Ara h 3. Anti-Ara h 3 antibodies reacted with two groups of protein peptides, one with strong reactions and another with weak reactions. These peptide spots with weak reaction on 2-D PAGE to anti-Ara h 3 antibodies are subunits or isoallergens of this potential peanut allergen iso-Ara h 3. A recent study suggested that Ara h 3 basic subunits may be more significant allergenicity than the acidic subunits.

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Chromosomal and phylogenetic context for conglutin genes in Arachis based on genomic sequence

Cited by 61 publications

References 50 publications

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

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

Temporal and Spatial Expression of the Major Allergens in Developing and Germinating Peanut Seed

Proteomic Analysis of Peanut Seed Storage Proteins and Genetic Variation in a Potential Peanut Allergen

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