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A high-continuity and annotated tomato reference genome
- Source :
- BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021), BMC Genomics
- Publication Year :
- 2021
- Publisher :
- Springer Science and Business Media LLC, 2021.
-
Abstract
- Background Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. Results Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. Conclusion Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.
- Subjects :
- QTL analysis
Sequence assembly
Computational biology
comparative genomics
Biology
QH426-470
Solanum
Genome
Domestication
Solanum lycopersicum
Genetics
Humans
high-density genetic map
Gene
Research
fungi
Chromosome Mapping
food and beverages
Genomics
Accession number (bioinformatics)
biology.organism_classification
de novo tomato genome
Functional genomics
TP248.13-248.65
Reference genome
Biotechnology
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 22
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....5b9cfec596212af147ea0bc57a3d475c