1
|
Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
Collapse
Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| |
Collapse
|
2
|
Font i Forcada C, Velasco L, Socias i Company R, Fernández i Martí Á. Association mapping for kernel phytosterol content in almond. Front Plant Sci 2015; 6:530. [PMID: 26217374 PMCID: PMC4496553 DOI: 10.3389/fpls.2015.00530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/29/2015] [Indexed: 05/21/2023]
Abstract
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.
Collapse
Affiliation(s)
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior Investigaciones CientíficasCórdoba, Spain
| | - Rafel Socias i Company
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de AragónZaragoza, Spain
| | - Ángel Fernández i Martí
- Genome Center, University of California, DavisDavis, CA, USA
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de AragónZaragoza, Spain
- *Correspondence: Ángel Fernández i Martí, Genome Center, University of California, 451 Health Sciences Dr., Davis, Davis, CA 95616, USA
| |
Collapse
|