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Articles by Ray Ming
Uncovering the mechanism of female restitution in sugarcane hybrids
Abstract Variations of meiosis, which normally halve genetic complements prior to fertilization, can have profound consequences. For example, whole-genome duplications (polyploidy) have shaped the evolution and diversification of most angiosperm lineages. The century-long success of sugarcane interspecific hybrids has been attributed to unusual female restitution—an unreduced maternal gamete fusing with a normal haploid paternal gamete1,2.
Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms
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Keywords Cunninghamia lanceolata gymnosperms genome evolution conifer whole-genome duplication Research topic(s) CP: plants CP: genomics Introduction Gymnosperms, encompassing extant taxa, such as cycads, Ginkgo, conifers, and gnetophytes1,2,3,4 first emerged during the Late Devonian period, approximately 360 million years ago (Mya).5 Despite their ancient origins, gymnosperms today comprise slightly over 1000 species, significantly fewer than the 354 000 angiosperm species.6 However, fossil...
By Si-Zu Lin, Yu Chen, Chao Wu, Wei-Hong Sun, Zhen Li, Jie-Yu Wang, Shu-bin Li, Zhi-Wen Wang, Wen-Chieh Tsai, Si-Ren Lan, Lei Yao, Yan Zhang, Jia-Jun Zhang, Xia Yu, Shan-Shan Xu, Peng-Fei Wu, Kai-Min Lin, Bao Liu, Li-Li Zhou, Ming Li, Peng Shuai, Xiao-Long Hou, Yi-Han Wu, Nuo Li, Sheng Xiong, Zhuang Zhou, Dan-Dan Zuo, Jia Li, Pei Wang, Jian Zhang, Ding-Kun Liu, Gui-Zhen Chen, Jie Huang, Yuan-Yuan Li, Xiang Zhao, Xue-Wen Zhang, Ying Yu, Zhi-Wei Liu, Ray Ming, Yves Van de Peer, Zhong-Jian Liu, Heng-Chi Chen, Chang-Mian Ji, Xiang-Qing Ma, Fei-Ping Zhang, Ya-Cong Xie, Meng-Meng Lü, Di-Yang Zhang, Yi-Quan Ye, Zhi-Hui Ma, Guo-Chang Ding, Guang-Qiu Cao, Zong-Ming He, Ai-Qin Liu, Yan-Qing Lin, Shao-Ning Ruan, Shi-Jiang Cao, Xue-Die Liu, Ming-Zhong Huang, Qin-Yao Zheng, Xue-Wei Zhao, Wen-Ying Zhong, Zheng-Bao Xia, Hong-Kun Zheng
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Cell Reports
Verified
A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing
Abstract Nutmeg (Myristica fragrans Houtt.) is a dioecious species that produces one of the most valuable spices and has peculiar holocentric chromosomes with diffuse centromere. The impact of holocentricity on the evolution of sex chromosomes is not well understood. Here, we present the first fully annotated haplotype-resolved chromosome-level genome of a male nutmeg plant, identify its sex chromosomes and analyse evolution of the sex-linked region (SLR).
Genetic architecture of sugarcane traits in a polyploid genomics framework
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Abstract Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10–12 sets of chromosomes). This complexity resulted from nobilization—a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts to elucidate the genetic basis of its considerable sucrose-storing capacity.
By Jungang Wang, Xiaofeng Li, Yibin Wang, Jishan Lin, Shuai Chen, Hongbo Liu, Xiao Chen, Kun Chai, Tingting Zhao, Ruijie Wu, Ping Zhao, Zhongqiang Xia, Shengcheng Zhang, Yi Liu, Shenyang Qu, Ziqi Ye, Yuhan Song, Qingyuan Deng, Xiaofei Zeng, Guangrun Yu, Ran Kong, Baoqing Zhang, Wei Zhang, Jun Mao, Xin Lu, Haifeng JIA, Xueting Zhao, Qianqian Zhang, Shuzhen Zhang, Wenwei Cai, Dongao Huo, Yuqing Gong, Shiqiang Huang, Yongji Huang, Zehuai Yu, Zuhu Deng, Baoshan Chen, Yuebin Zhang, Muqing M. Zhang, Ray Ming, Xingtan Zhang, Aoqian Dong, Cuilian Feng, Yaodong Zheng, Peifang Zhao
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Nature
Verified
Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis - Nature Communications
Abstract Accessory chromosomes are non-essential for growth but poorly characterized in basidiomycetes, unlike in Ascomycota. Here, we report whole-genome sequencing of 16 strains of the basidiomycete Tremella fuciformis (silver ear fungus), generating 27 complete haplotypes (5 monokaryons and 11 dikaryons, each contributing two distinct haplotypes). Genome size varied by over one-third, driven by accessory chromosomes and repetitive sequences in core chromosomes (essential for basic biology).
Allele-Specific Hormone Dynamics in Highly Transgressive F2 Biomass Segregants in Sugarcane (Saccharum spp.)
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Harnessing Genetic Tools for Sustainable Bioenergy: A Review of Sugarcane Biotechnology in Biofuel Production
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Author Correction: The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence - Nature Plants
Correction to: Nature Plants https://doi.org/10.1038/s41477-022-01146-6, published online 9 May 2022. In the version of the article initially published, Dipak Khadka, who collected the samples in Nepal, was thanked in the Acknowledgements instead of being listed as an author. His name and affiliation (GoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal) have been added to the authorship in the HTML and PDF versions of the article.
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits - Nature Genetics
Abstract The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae.
A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus - Nature Plants
Author notes These authors contributed equally: Tianyou Wang, Baiyu Wang, Xiuting Hua, Haibao Tang.
SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya - Nature Genetics
Abstract Transgenic papaya is widely publicized for controlling papaya ringspot virus. However, the impact of particle bombardment on the genome remains unknown. The transgenic SunUp and its progenitor Sunset genomes were assembled into 351.5 and 350.3 Mb in nine chromosomes, respectively. We identified a 1.64 Mb insertion containing three transgenic insertions in SunUp chromosome 5, consisting of 52 nuclear-plastid, 21 nuclear-mitochondrial and 1 nuclear genomic fragments.
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence - Nature Plants
Abstract To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns.
The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa)
Introduction Strawberry is a major specialty crop cultivated worldwide for its sweet and flavorful receptacle, which is referred to commonly as a fruit. Strawberry is under intense breeder selection for new cultivars based on diverse traits. These include receptacle color, firmness, sweetness, yield, flowering time, shipping quality, shelf life, nutrition, flavors, aromas, and disease resistance.
Analysis of MADS-box genes revealed modified flowering gene network and diurnal expression in pineapple
Abstract Background Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological processes. However, there is no systematic analysis of MADS-box family genes in pineapple (Ananas comosus). Results Forty-eight MADS-box genes were identified in the pineapple genome.
Pineapple genome sequences hint at plant domestication in single step
As their Latin name indicates, pineapples are truly “excellent fruits”—and thanks to a freshly completed genome sequencing project, researchers have gained a new understanding of how human agriculture has shaped the evolution of this and other crops. An international team led by University of Illinois Professor of Plant Biology Ray Ming (GEGC) published their analysis of the genome of the red pineapple, a plant grown for fiber production and as an ornamental, in Nature Genetics.
The pineapple genome and the evolution of CAM photosynthesis
The genome of pineapple variety F153, cultivated by Del Monte for 80 years, was sequenced and assembled using 400× Illumina reads, 2× Moleculo synthetic long reads, 1× 454 reads, 5× PacBio single-molecule long reads and 9,400 BACs. Because of self-incompatibility, pineapple has high levels of heterozygosity and is cultivated through clonal propagation.
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