Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding
| Autor: | Mark Timothy Rabanus-Wallace, Sergio Lanteri, Giuseppe Leonardo Rotino, Sudharsan Padmarasu, Nils Stein, Laura Toppino, Giovanni Giuliano, Lorenzo Barchi, Ezio Portis, Jaime Prohens |
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| Přispěvatelé: | Barchi, L., Rabanus-Wallace, M. T., Prohens, J., Toppino, L., Padmarasu, S., Portis, E., Rotino, G. L., Stein, N., Lanteri, S., Giuliano, G. |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine pan‐plastome Nuclear gene pan-plastome whole-genome resequencing Plant Science whole‐genome resequencing Genes Plant 01 natural sciences pan‐genome Polymorphism Single Nucleotide 03 medical and health sciences domestication Quantitative Trait Heritable single nucleotide polymorphism Genetic variation Genetics Solanum incanum Solanum melongena Gene 2. Zero hunger Genetic diversity eggplant wild relatives biology Whole Genome Sequencing food and beverages Chromosome Mapping Genetic Variation Cell Biology Original Articles biology.organism_classification indel eggplant wild relatives 02.- Poner fin al hambre conseguir la seguridad alimentaria y una mejor nutrición y promover la agricultura sostenible Plant Breeding GENETICA 030104 developmental biology indel genome assembly Original Article pan-genome Solanum domestication genome assembly indel eggplant wild relatives pan-genome pan-plastome single nucleotide polymorphism Solanum melongena whole-genome resequencing Solanaceae Genome Plant 010606 plant biology & botany Reference genome |
| Zdroj: | The Plant Journal |
| DOI: | 10.1111/tpj.15313 |
| Popis: | Summary Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non‐anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant ‘67/3’ reference line, by Hi‐C retrofitting of a previously released short read‐ and optical mapping‐based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome‐level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan‐genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan‐plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present‐day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant. Significance Statement Chromosome conformation capture (Hi‐C) was applied for improving a short read‐based genome assembly of eggplant (Solanum melongena). The enhanced assembly, combined with resequencing data of accessions representing the genetic and phenotypic diversity of the species and of its closest wild relatives, allowed the construction of the first eggplant pan‐genome and pan‐plastome and the identification of selective sweeps and candidate genes likely involved in eggplant domestication and breeding. |
| Databáze: | OpenAIRE |
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