The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal‐Bertioli, Soraya C. M.; Ren, Lihui; Farmer, Andrew; Pandey, Manish K.; Samoluk, Sergio Sebastián; Abernathy, Brian; Agarwal, Gaurav; Ballén‐Taborda, Carolina; Cameron, Connor; Campbell, Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; Baidouri, Moaine El; Guo, Bao‐Zhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher; Mirouze, Marie; Moretzsohn, Márcio de Carvalho; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, E; Michelmore, Richard W.; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K. S.; Scheffler, Brian E.; Grimwood, Jane; Ozias‐Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz, Jeremy

doi:10.1038/s41588-019-0405-z

Cited by 520 publications

(629 citation statements)

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“…Green marks on the chromosome backbones (e.g. tops of A05 and B05) show the locations of large-scale subgenome invasion, observed in the Tifrunner genome assembly (Bertioli et al, 2019). Table 1 Counts of genetically unique samples, relative to phenotypic traits.…”

Section: Discussionmentioning

confidence: 99%

“…Base-calls were also derived computationally for four sequenced Arachis genomes: A. duranensis, A. ipaënsis (Bertioli et al 2016) and A. hypogaea varieties Tifrunner (Bertioli et al 2019), Shitouqi (Zhuang et al 2019), and Fuhuasheng . Base-calls from the genomic sequences were made by aligning flanking sequences plus the variant base, using two sequences per variant per locus, to the respective genome, using blastn (Altschul et al 1990).…”

Section: Diversity Phylogenetic and Network Analysismentioning

confidence: 99%

“…Clade 4 is much less mixed geographically, coming predominantly from central and western South America ( Figure 6). Peanut's geographic origin (through the initial instance of tetraploidy) has been convincingly established as having occurred in (Bertioli et al 2016;Bertioli et al 2019)southeastern Bolivia/northwestern Argentina (Bertioli et al 2016;Bertioli et al 2019 in ancient times, and still important locally, being found in Peruvian markets, for example. These highly reticulated pod types are also seen in multiple archaeological sites on the coast of Peru and Chile, and Argentina (Masur et al 2018;Krapovickas 1995), as well as in early European herbarium specimens.…”

Section: The Geographic Distribution Of Genotypesmentioning

confidence: 99%

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Genotypic characterization of the U.S. peanut core collection

Otyama

Kulkarni

Chamberlin

et al. 2020

Preprint

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Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin.The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions.the genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut's rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

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Section: Discussionmentioning

confidence: 99%

Section: Diversity Phylogenetic and Network Analysismentioning

confidence: 99%

Section: The Geographic Distribution Of Genotypesmentioning

confidence: 99%

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Genotypic characterization of the U.S. peanut core collection

Otyama

Kulkarni

Chamberlin

et al. 2020

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“…Genomic mapping of the cultivated allotetraploid peanut was recently completed through an international effort (Bertioli et al, 2019). These Table 5.…”

Section: Genotypementioning

confidence: 99%

Inheritance of a Novel Heterozygous Peanut Mutant, 5-Small Leaflet

Branch

Tallury²,

Clevenger

et al. 2020

Peanut Science

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An unusual 5-Small Leaflet mutant plant was found within the 'Georgia Green' runner-type peanut (Arachis hypogaea L.) cultivar. Subsequent selfing has not established a true-breeding 5-Small Leaflet genotype. It continues to segregate normal and 5-Small Leaflet plants but with a reduced number of normal leaf plants upon selection for 5-Small Leaflet phenotypes after several self-generations. F 1 , F 2 , F 3 , and F 4 data suggests that the 5-Small Leaflet trait is dominant or possibly pseudo-dominant. Likewise, the 5-Small Leaflet mutant can only be used as a pollen parent in crosses, and it has approximately a 1:1 ratio of elongated to normal stigmas, respectively, on individual plants. This is an example of a novel heterozygous peanut mutant plant found within the cultivated allotetraploid peanut.

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“…Although the number of genome sequences which take the advantages of both second and third generation sequencing are increasing (11)(12)(13), the majority of genome assemblies available from the National Center of Biotechnology Information (NCBI) were generated predominantly using short reads from the second-generation technology.…”

Section: Introductionmentioning

confidence: 99%

Read coverage as an indicator of misassembly in a short-read based genome assembly

Wang

Meng

Moore

et al. 2019

Preprint

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the original research plans; F.M. and P.W. conducted the bulk of the computational analysis; B.M. assisted with the machine learning models; P.W. and S.-H.S. wrote the manuscript with contributions of all the authors; S.-H.S. agrees to serve as the author responsible for contact and ensures communication. AbstractAvailability of genome sequences has led to significant progress in biological sciences and beyond. With few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies. While extremely useful, the short-read coverages across the assemblies are highly uneven, indicative of sequencing and assembly issues. To assess the underlying causes of such uneven read coverage, we used the tomato genome as an example and integrated multiple sequence features to establish machine learning models capable of predicting whether a genomic region has significantly high or low read coverage. Importantly, 0.6% (5.1Mb) and 9.7% (79.6Mb) of tomato genome assembly had significantly higher and lower coverage compared to background, respectively. By evaluating features important for the prediction, we found that GC content and high density of transposon elements are the major contributors to break points in an assembly, leading to gaps filled with Ns and the resulting low read coverages. In contrast, simple sequence repeats and tandemly duplicated genes, especially specialized metabolism genes, tend to be mis-assembled, resulting in high read coverages. We also present evidence of a misassembled regions containing tandemly duplicated specialized metabolism genes. The presence of variable coverage regions is expected to significantly impact genome-wide studies, highlighting the need to detect them in short-read based assemblies.

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The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Cited by 520 publications

References 80 publications

Genotypic characterization of the U.S. peanut core collection

Genotypic characterization of the U.S. peanut core collection

Inheritance of a Novel Heterozygous Peanut Mutant, 5-Small Leaflet

Read coverage as an indicator of misassembly in a short-read based genome assembly

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