title: The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.
abstract: Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.
authors.affiliation: College of Forestry, Northwest A&F University, Yangling, China.|Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, China.
authors.forename: Jian
authors.identifier: http://orcid.org/0000-0001-7945-5355
authors.initials: J
authors.lastname: Huang
authors.affiliation: College of Forestry, Northwest A&F University, Yangling, China.|Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, China.
authors.forename: Chunmei
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Boyce Thompson Institute, Cornell University, Ithaca, New York, United States of America.
authors.forename: Zhangjun
authors.identifier: http://orcid.org/0000-0001-9684-1450
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: KangKang
authors.initials: K
authors.lastname: Wan
authors.affiliation: College of Forestry, Northwest A&F University, Yangling, China.|Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Pang
authors.affiliation: College of Forestry, Northwest A&F University, Yangling, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yin
authors.affiliation: Boyce Thompson Institute, Cornell University, Ithaca, New York, United States of America.
authors.forename: Yang
authors.initials: Y
authors.lastname: Bai
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Sun
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
authors.forename: Lizhi
authors.initials: L
authors.lastname: Gao
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Jinbo
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Forestry, Northwest A&F University, Yangling, China.|Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, China.
authors.forename: Xingang
authors.identifier: http://orcid.org/0000-0001-7945-5355
authors.initials: X
authors.lastname: Li
mesh_terms: D002874:Chromosome Mapping; D000071278:Domestication; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics*; D018745:Genome, Plant; D023281:Genomics; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D016415:Sequence Alignment; D013649:Taste / Q000235:genetics*; D031957:Ziziphus / Q000235:genetics*