Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding.

The Plant Journal : for Cell and Molecular Biology
Lorenzo BarchiGiovanni Giuliano

Abstract

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 selecti...Continue Reading

References

Nov 20, 2001·Nucleic Acids Research·S KurtzR Giegerich
Apr 5, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·A FraryS D Tanksley
Jul 12, 2003·Bioinformatics·Michael BrudnoSerafim Batzoglou
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hervé TettelinClaire M Fraser
Jul 11, 2006·Journal of Molecular Evolution·Sabine KahlauRalph Bock
Jul 18, 2006·Nucleic Acids Research·Mario StankeBurkhard Morgenstern
Apr 28, 2007·Bioinformatics·Robert KoflerTamas Lelley
May 29, 2007·Nucleic Acids Research·Yana Bromberg, Burkhard Rost
Dec 18, 2008·Current Opinion in Microbiology·Hervé TettelinDuccio Medini
Aug 8, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tsukasa NunomeHiroyuki Fukuoka
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 21, 2010·Genome Research·Hua ChenDavid Reich
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nicholas D PattengaleAlexandros Stamatakis
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Dec 6, 2011·Nucleic Acids Research·Philippe LameschEva Huala
Feb 4, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Koji MiyatakeHiroyuki Fukuoka
Feb 22, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hiroyuki FukuokaAkio Ohyama
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jun 5, 2012·Nature·UNKNOWN Tomato Genome Consortium
Oct 2, 2012·Bioinformatics·Ming HuJun S Liu
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 5, 2013·Nature Biotechnology·Joshua N BurtonJay Shendure
Jan 15, 2014·Bioinformatics·Yongbing ZhaoJingfa Xiao
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Sep 23, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki HirakawaHiroyuki Fukuoka

❮ Previous
Next ❯

Citations

Oct 27, 2021·The Plant Journal : for Cell and Molecular Biology·Xiaohui JiangWeiwei Wen

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Dandan LiYikui Wang
The Journal of Allergy and Clinical Immunology
Siddanakoppalu N Pramod, Yeldur P Venkatesh
DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Hideki HirakawaHiroyuki Fukuoka
© 2021 Meta ULC. All rights reserved