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Open AccessGraph-based pangenomics maximizes genoty** density and reveals structural impacts on fungal resistance in melon
The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyp...
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Article
TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.)
Telomeres are the physical ends of eukaryotic linear chromosomes that play critical roles in cell division, chromosome maintenance, and genome stability. In many plants, telomeres are comprised of TTTAGGG tand...
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Evaluating two different models of peanut’s origin
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Open AccessThe genome sequence of segmental allotetraploid peanut Arachis hypogaea
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report ...
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Article
Open AccessImproved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA
Cold shock proteins (CSPs) enhance acclimatization of bacteria to adverse environmental circumstances. The Escherichia coli CSP genes CspA and CspB were modified to plant-preferred codon sequences and named as Se...
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Open AccessThe genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
David Bertioli and colleagues report the genomes of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut, Arachis hypogaea. Their analyses are a first step in understanding the evol...
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Article
Open AccessLandscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the...
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Open AccessTILLING by sequencing to identify induced mutations in stress resistance genes of peanut (Arachis hypogaea)
Targeting Induced Local Lesions in Genomes (TILLING) is a powerful reverse genetics approach for functional genomics studies. We used high-throughput sequencing, combined with a two-dimensional pooling strateg...
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Article
Open AccessTranscriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance
Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-...
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Article
Distribution and analysis of SSR in mung bean (Vigna radiata L.) genome based on an SSR-enriched library
Simple sequence repeats (SSR) are widely distributed in plant genomes, have been popular genetic markers and can be involved in gene function. We report an SSR analysis of mung bean (Vigna radiata L.), based on ...
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Open AccessA reference genome for common bean and genome-wide analysis of dual domestications
Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene po...
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Open AccessDynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents
Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome....
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Erratum: Genome sequence of the palaeopolyploid soybean
Nature 463, 178–183 (2010) During resubmission of this work, a paper was published1 that used a comparative genomics approach between soybean and maize to show that a single-base mutation in chromosome 19 acco...
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Open AccessGenome sequence of the palaeopolyploid soybean
Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the...
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Open AccessIntegration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding...
