Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
Xia Wang,Yuantao Xu,Siqi Zhang,Li Cao,Yue Huang,Junfeng Cheng,Guizhi Wu,Shilin Tian,Chunli Chen,Yan Liu,Huiwen Yu,Xiaoming Yang,Hong Lan,Nan Wang,Lun Wang,Jidi Xu,Xiaolin Jiang,Zongzhou Xie,Meilian Tan,Robert M. Larkin,Ling-Ling Chen,Bin-Guang Ma,Yijun Ruan,Xiuxin Deng,Qiang Xu +24 more
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TLDR
This study de novo sequenced and comprehensively studied the genomes of four representative citrus species and found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony.Abstract:
Qiang Xu and colleagues sequence four citrus species de novo, along with 100 accessions, including primitive, wild and cultivated citrus. Their genomic analyses associate the CitRWP gene with polyembryony and suggest that regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. The emergence of apomixis—the transition from sexual to asexual reproduction—is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.read more
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Genomics of the origin and evolution of Citrus
Guohong Albert Wu,Javier Terol,Victoria Ibanez,Antonio López-García,Estela Pérez-Román,Carles Borredá,Concha Domingo,Francisco R. Tadeo,José Carbonell-Caballero,Roberto Alonso,Franck Curk,Dongliang Du,Patrick Ollitrault,Mikeal L. Roose,Joaquín Dopazo,Frederick G. Gmitter,Daniel S. Rokhsar,Daniel S. Rokhsar,Daniel S. Rokhsar,Manuel Talon +19 more
TL;DR: Ten natural citrus species are described, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and it is proposed that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons.
Journal ArticleDOI
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Caroline Belser,Benjamin Istace,Erwan Denis,Marion Dubarry,Franc-Christophe Baurens,Cyril Falentin,Mathieu Genete,Wahiba Berrabah,Anne-Marie Chèvre,Régine Delourme,Gwenaëlle Deniot,Philippe Duffé,Stefan Engelen,Arnaud Lemainque,Maria J. Manzanares-Dauleux,Guillaume Martin,Jérôme Morice,Benjamin Noel,Xavier Vekemans,Angélique D'Hont,Mathieu Rousseau-Gueutin,Valérie Barbe,Corinne Cruaud,Patrick Wincker,Jean-Marc Aury +24 more
TL;DR: A strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies is described and demonstrated applicability by generating high-quality genome sequences for two new dicotyledon morphotypes.
Journal ArticleDOI
The structure and function of the global citrus rhizosphere microbiome.
Jin Xu,Yunzeng Zhang,Yunzeng Zhang,Pengfan Zhang,Pankaj Trivedi,Nadia Riera,Yayu Wang,Xin Liu,Guangyi Fan,Ji-Liang Tang,Helvécio D. Coletta-Filho,Jaime Cubero,Xiaoling Deng,Veronica Ancona,Zhanjun Lu,Balian Zhong,M. Caroline Roper,Nieves Capote,Vittoria Catara,Gerhard Pietersen,Christian Vernière,Abdullah M. Al-Sadi,Lei Li,Fan Yang,Xun Xu,Jian Wang,Huanming Yang,Tao Jin,Nian Wang +28 more
TL;DR: A comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome is reported, using both amplicon and deep shotgun metagenomic sequencing of samples collected across six continents to help guide microbial isolation and culturing and to harness the power of the microbiome to improve plant production and health.
Journal ArticleDOI
Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication.
TL;DR: The population history of grapes is estimated and it is confirmed that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness, which solves three ongoing mysteries about plant domestication.
Journal ArticleDOI
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.
Maximilian Schmidt,Alexander Vogel,Alisandra K. Denton,Benjamin Istace,Alexandra Wormit,Henri van de Geest,Marie E. Bolger,Saleh Alseekh,Janina Maß,Christian Pfaff,Ulrich Schurr,Roger T. Chetelat,Florian Maumus,Jean-Marc Aury,Sergey Koren,Alisdair R. Fernie,Daniel Zamir,Anthony Bolger,Bjoern Usadel,Bjoern Usadel +19 more
TL;DR: The generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii indicates that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
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