Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Grabowski, Paul P.; Dang, Phat; Jenkins, Jerry J.; Sreedasyam, Avinash; Webber, Jenell; Lamb, Marshall; Zhang, Qiong; Sanz-Saez, Alvaro; Feng, Yucheng; Bunting, Victoria; Talag, Jayson; Clevenger, Josh; Ozias-Akins, Peggy; Holbrook, C. Corley; Chu, Ye; Grimwood, Jane; Schmutz, Jeremy; Chen, Charles; Lovell, John T.

doi:10.1093/g3journal/jkae208

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Journal Article · Sun Sep 01 00:00:00 EDT 2024 · G3

DOI:https://doi.org/10.1093/g3journal/jkae208· OSTI ID:2479207

^[1]; Dang, Phat ^[2]; ^[1]; ^[1]; Webber, Jenell ^[1]; Lamb, Marshall ^[2]; Zhang, Qiong ^[3]; Sanz-Saez, Alvaro ^[3]; Feng, Yucheng ^[3]; Bunting, Victoria ^[4]; Talag, Jayson ^[4]; ^[1]; Ozias-Akins, Peggy ^[5]; Holbrook, C. Corley ^[6]; ^[5]; ^[1]; ^[7]; Chen, Charles ^[3]; ^[7]

HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
National Peanut Research Laboratory, USDA-ARS, Dawson, GA (United States)
Auburn University College of Agriculture, AL (United States)
University of Arizona, Tucson, AZ (United States)
University of Georgia, Tifton, GA (United States)
Crop Genetics and Breeding Research Unit, USDA-ARS, Tifton, GA (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for “Line8,” a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: NIFA (National Institute of Food and Agriculture); National Peanut Board; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2479207

Alternate ID(s):: OSTI ID: 2488369

Journal Information:: G3, Journal Name: G3 Journal Issue: 11 Vol. 14; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

References (41)

BUSCO: Assessing Genomic Data Quality and Beyond Manni, Mosè; Berkeley, Matthew R.; Seppey, Mathieu Current Protocols, Vol. 1, Issue 12 https://doi.org/10.1002/cpz1.323	journal	December 2021
Tolerance to mid‐season drought in peanut can be achieved by high water use efficiency or high efficient use of water Zhang, Qiong; Dang, Phat; Chen, Charles Crop Science, Vol. 62, Issue 5 https://doi.org/10.1002/csc2.20806	journal	July 2022
Peanuts as functional food: a review Arya, Shalini S.; Salve, Akshata R.; Chauhan, S. Journal of Food Science and Technology, Vol. 53, Issue 1 https://doi.org/10.1007/s13197-015-2007-9	journal	September 2015
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments Durand, Neva C.; Shamim, Muhammad S.; Machol, Ido Cell Systems, Vol. 3, Issue 1 https://doi.org/10.1016/j.cels.2016.07.002	journal	July 2016
Functional components of peanuts (Arachis Hypogaea L.) and health benefits: A review Çiftçi, S.; Suna, G. Future Foods, Vol. 5 https://doi.org/10.1016/j.fufo.2022.100140	journal	June 2022
Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement Chen, Xiaoping; Lu, Qing; Liu, Hao Molecular Plant, Vol. 12, Issue 7 https://doi.org/10.1016/j.molp.2019.03.005	journal	July 2019
The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut Bertioli, David John; Cannon, Steven B.; Froenicke, Lutz Nature Genetics, Vol. 48, Issue 4 https://doi.org/10.1038/ng.3517	journal	February 2016
The genomic landscape of molecular responses to natural drought stress in Panicum hallii Lovell, John T.; Jenkins, Jerry; Lowry, David B. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07669-x	journal	December 2018
Haplotype-resolved assembly of diploid genomes without parental data Cheng, Haoyu; Jarvis, Erich D.; Fedrigo, Olivier Nature Biotechnology, Vol. 40, Issue 9 https://doi.org/10.1038/s41587-022-01261-x	journal	March 2022
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication Zhuang, Weijian; Chen, Hua; Yang, Meng Nature Genetics, Vol. 51, Issue 5 https://doi.org/10.1038/s41588-019-0402-2	journal	May 2019
The genome sequence of segmental allotetraploid peanut Arachis hypogaea Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh Nature Genetics, Vol. 51, Issue 5 https://doi.org/10.1038/s41588-019-0405-z	journal	May 2019
Evaluating two different models of peanut’s origin Bertioli, David J.; Abernathy, Brian; Seijo, Guillermo Nature Genetics, Vol. 52, Issue 6 https://doi.org/10.1038/s41588-020-0626-1	journal	May 2020
Gene expression profiling describes the genetic regulation of Meloidogyne arenaria resistance in Arachis hypogaea and reveals a candidate gene for resistance Clevenger, Josh; Chu, Ye; Arrais Guimaraes, Larissa Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-00971-6	journal	May 2017
Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms Bhogireddy, Sailaja; Xavier, Abishek; Garg, Vanika Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-60187-z	journal	March 2020
Evaluation of five peanut (Arachis hypogaea) genotypes to identify drought responsive mechanisms utilising candidate-gene approach Dang, Phat M.; Chen, Charles Y.; Holbrook, C. Corley Functional Plant Biology, Vol. 40, Issue 12 https://doi.org/10.1071/FP13116	journal	January 2013
Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange Bertioli, David J.; Clevenger, Josh; Godoy, Ignacio J. Proceedings of the National Academy of Sciences, Vol. 118, Issue 38 https://doi.org/10.1073/pnas.2104899118	journal	September 2021
New strategies to improve minimap2 alignment accuracy Li, Heng Bioinformatics, Vol. 37, Issue 23 https://doi.org/10.1093/bioinformatics/btab705	journal	October 2021
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
Fast and SNP-tolerant detection of complex variants and splicing in short reads Wu, T. D.; Nacu, S. Bioinformatics, Vol. 26, Issue 7, p. 873-881 https://doi.org/10.1093/bioinformatics/btq057	journal	February 2010
Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar Grabowski, Paul P.; Dang, Phat; Jenkins, Jerry J. G3: Genes, Genomes, Genetics, Vol. 14, Issue 11 https://doi.org/10.1093/g3journal/jkae208	journal	September 2024
Twelve years of SAMtools and BCFtools Danecek, Petr; Bonfield, James K.; Liddle, Jennifer GigaScience, Vol. 10, Issue 2 https://doi.org/10.1093/gigascience/giab008	journal	January 2021
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Haas, B. J. Nucleic Acids Research, Vol. 31, Issue 19 https://doi.org/10.1093/nar/gkg770	journal	October 2003
Phytozome: a comparative platform for green plant genomics Goodstein, David M.; Shu, Shengqiang; Howson, Russell Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr944	journal	November 2011
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data McKenna, A.; Hanna, M.; Banks, E. Genome Research, Vol. 20, Issue 9 https://doi.org/10.1101/gr.107524.110	journal	July 2010
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Koboldt, D. C.; Zhang, Q.; Larson, D. E. Genome Research, Vol. 22, Issue 3 https://doi.org/10.1101/gr.129684.111	journal	February 2012
Fast and accurate de novo genome assembly from long uncorrected reads Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.214270.116	journal	January 2017
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems Vasimuddin, Md.; Misra, Sanchit; Li, Heng 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) https://doi.org/10.1109/IPDPS.2019.00041	conference	May 2019
Variabilities in symbiotic nitrogen fixation and carbon isotope discrimination among peanut (Arachis hypogaea L.) genotypes under drought stress Wang, Xu; Chen, Charles Y.; Dang, Phat Journal of Agronomy and Crop Science, Vol. 209, Issue 2 https://doi.org/10.1111/jac.12619	journal	July 2022
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds Dudchenko, Olga; Batra, Sanjit S.; Omer, Arina D. Science, Vol. 356, Issue 6333 https://doi.org/10.1126/science.aal3327	journal	March 2017
Automated generation of heuristics for biological sequence comparison Slater, Guy St C.; Birney, Ewan BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-31	journal	February 2005
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies Goel, Manish; Sun, Hequan; Jiao, Wen-Biao Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1911-0	journal	December 2019
LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology Driguez, Patrick; Bougouffa, Salim; Carty, Karen Genome Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s13059-021-02475-z	journal	September 2021
Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing Corbett-Detig, Russell B.; Said, Iskander; Calzetta, Maria Genetics, Vol. 213, Issue 4 https://doi.org/10.1534/genetics.119.302385	journal	December 2019
Registration of ‘Georgia Green’ Peanut Branch, W. D. Crop Science, Vol. 36, Issue 3 https://doi.org/10.2135/cropsci1996.0011183X003600030051x	journal	May 1996
Supplemental Material for Grabowski et al., 2024 Grabowski, Paul P.; Dang, Phat; J. Jenkins, Jerry GSA Journals https://doi.org/10.25387/g3.26530861	dataset	January 2024
Use of Wild Arachis Species/Introgression of Genes into A. hypogaea L. Simpson, C. E. Peanut Science, Vol. 28, Issue 2 https://doi.org/10.3146/i0095-3679-28-2-12	journal	January 2001
Transcriptome Profile Reveals Drought-Induced Genes Preferentially Expressed in Response to Water Deficit in Cultivated Peanut (Arachis hypogaea L.) Wang, Xu; Yang, Xinlei; Feng, Yucheng Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.645291	journal	April 2021
Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers Newman, Cassondra S.; Andres, Ryan J.; Youngblood, Ramey C. Frontiers in Plant Science, Vol. 13 https://doi.org/10.3389/fpls.2022.1073542	journal	January 2023
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w Cingolani, Pablo; Platts, Adrian; Wang, Le Lily Fly, Vol. 6, Issue 2 https://doi.org/10.4161/fly.19695	journal	April 2012
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes Lovell, John T.; Sreedasyam, Avinash; Schranz, M. Eric eLife, Vol. 11 https://doi.org/10.7554/eLife.78526	journal	September 2022

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Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

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