Shuangxia Jin

Shuangxia Jin
Huazhong Agricultural University | HZAU · National Key Laboratory of Crop Genetic Improvement

phD/Full Professor

About

110
Publications
38,330
Reads
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4,368
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Introduction
Dr. Shuangxia Jin is a full professor of Huazhong Agricultural University, China. Dr. Jin have been working in plant biotechnology for 20 years, his current research involves in Insects and cotton host molecular interaction, genome editing, plant genomics. Dr. Jin published more than 60 peer reviewed papers in journals such as Genome Bio., Adv. Sci., Nature Commun., TIPS, Plant Physiol., New Phytologist, PBJ etc. He is the Senior Editor of PBJ and Associate Editor of Crop Journal , Plants.
Additional affiliations
December 2015 - present
Huazhong Agricultural University
Position
  • Managing Director
November 2007 - March 2012
University of Central Florida
Position
  • Research Assistant
June 2006 - present
Huazhong Agricultural University
Position
  • PI working on insect and plant host interaction

Publications

Publications (110)
Article
Full-text available
Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its hi...
Article
Full-text available
Life sciences have been revolutionized by genome editing (GE) tools, including zinc finger nucleases, transcription activator‐Like effector nucleases, and CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas (CRISPR‐associated) systems, which make the targeted modification of genomic DNA of all organisms possible. CRISPR/Cas syst...
Article
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Background: Wintersweet (Chimonanthus praecox), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecular mechanisms underlying these traits are largely unknown in this species. In addition, wintersweet is also a typical repres...
Article
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Background Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. Results We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb...
Article
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Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochr...
Article
Tobacco bacterial wilt caused by Ralstonia solanacearum invades tobacco plants during the whole growth period affecting yield and quality. However, the transcriptome profiling of tobacco plant in response to bacterial wilt has not been well studied. In this study, we identified the transcriptional profiles of bacterial wilt-resistant (ac Yanyan97)...
Article
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Many genes encoding nucleotide‐binding leucine‐rich repeat receptors (NLRs) are regulated and fine‐tuned by miR482 to balance the trade‐off between disease resistance and growth. Dicotyledonous plants, including cotton, usually have multiple miR482 isoforms. Each miR482 isoform can regulate several NLRs that in turn can be regulated by several diff...
Article
Section Oleifera (Theaceae) has attracted attention owing to the high levels of unsaturated fatty acids in seeds. Here, we reported the chromosome‐scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed...
Article
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Sap-sucking insects cause severe damage to cotton production. Long non-coding RNAs (lncRNAs) play vital regulatory roles in various development processes and stress response, however, the function of lncRNAs during sap-sucking insect infection in cotton is largely unknown. In this study, the transcriptome profiles between resistant (HR) and suscept...
Article
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Background Base editors (BEs) display diverse applications in a variety of plant species such as Arabidopsis, rice, wheat, maize, soybean, and cotton, where they have been used to mediate precise base pair conversions without the collateral generation of undesirable double-stranded breaks (DSB). Studies of single-nucleotide polymorphisms (SNPs) und...
Article
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Background Cotton fiber is an important natural resource for textile industry and an excellent model for cell biology study. Application of glabrous mutant cotton and high-throughput sequencing facilitates the identification of key genes and pathways for fiber development and cell differentiation and elongation. LncRNA is a type of ncRNA with more...
Article
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As the basic building blocks of all living species, cells play a crucial role in sustaining life activities. Traditional bulk methods only give us molecular insight into tissue, organ or/and individual. With the rapid development of sequencing technology, especially the 10X Genomics based on microfluidic omics, biological research has entered the e...
Article
Polyamines (PAs), especially spermidine and spermine (which are involved in various types of abiotic stress tolerance), have been reported in many plant species. In this study, we identified 14 putative S-adenosylmethionine decarboxylase genes (GhSAMDC1-14) in upland cotton. Based on phylogenetic and expression analyses conducted under different ab...
Article
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Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a rapidly increasing human population. Chemical weed control (herbicides...
Article
Abiotic stresses such as drought, salinity, and heat affect plant growth and development. Karelinia caspica is a unique perennial herb that grows in desert area for a long time and has strong tolerance to environmental stresses. In order to explore the functions of the Na+/H+ antiporter gene from eremophyte K. caspica (KcNHX1) in the abiotic stress...
Article
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Cellulose is one of the most abundant organic polymers in nature. It contains multiple β‐1,4‐glucan chains synthesized by cellulose synthases (CesAs) on the plasma membrane of higher plants. CesA subunits assemble into a pseudo‐6‐fold symmetric cellulose synthase complex (CSC), known as a ‘rosette complex’. The structure of CesA remains enigmatic....
Article
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Background Upland cotton ( Gossypium hirsutum ), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locu...
Article
Full-text available
Panax notoginseng (2n = 2x = 24), reputed as a valuable medicinal plant, belongs to the Araliaceae family(Figure 1a). P. notoginseng has been used as a traditional Chinese medicine with obvious efficacy and favorable safety. Currently, P. notoginseng is an important material of many well-known Chinese patent medicines including Xuesaitong, Yunnan B...
Article
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Free‐living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil, starch/sugar crop ch...
Article
Plant bugs (Miridae species) have become major agricultural pests that cause increasing and severe economic damage. Plant‐mediated RNA interference (RNAi) is emerging as an eco‐friendly, efficient, and reliable strategy for pest management. In this study, we isolated and characterized a lethal gene of Apolygus lucorum and named it Apolygus lucorum...
Article
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Background Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown. Results In this...
Preprint
Full-text available
Background: Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome consists of A and D subgenomes. The genes in have multiple copies with high sequence similarity that makes genetic, genomic and functional analysis extremely challenging. The recent accessibility of CRISPR/Cas9 tool offers the ability to modify targeted locus...
Article
Full-text available
Cotton (Gossypium hirsutum), the most important cash crop for natural textile fibers, meanwhile, represents the fifth largest source of vegetable oil for human consumption in the world. Typically, cottonseed oil contains three major fatty acids: 26% palmitic acid, 15% oleic acid, and 58% linoleic acid (Liu et al., 2002). The relatively high level o...
Article
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Polyamines play essential roles in plant development and various stress responses. In this study, one of the cotton S-adenosylmethionine decarboxylase (SAMDC) genes, GhSAMDC1, was constructed in the pGWB17 vector and overexpressed in tobacco. Leaf area and plant height increased 25.9–36.6% and 15.0–27.0%, respectively, compared to the wild type, an...
Article
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Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high‐quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 Kb;...
Article
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Cotton (Gossypium hirsutum) is an allotetraploid species and a typical thermophilic crop that can survive and grow well under temperatures up to 45°C. CRISPR/LbCpf1 (LbCas12a) is a temperature‐sensitive system for plant genome editing (Malzahn et al., 2019) and has been successfully applied in species such as rice, soybean, tobacco, maize and cotto...
Article
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The rapid rise in mean global temperature as a result of global warming threatens plant productivity (Li et al., 2015). Chloroplasts and chloroplast proteins are associated with environmental stresses (Alexia et al., 2019; Hong et al., 2020). Many heat shock proteins (HSPs) associate with chloroplast development and improve plant tolerance to heat...
Preprint
Full-text available
• Background • Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. • Results • In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages dur...
Article
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The CRISPR/Cas9 and Cas12a (Cpf1) tools have been used on a large scale for genome editing. A new effector with a single nuclease domain, a relatively small size, low frequency off‐target effects and cleavage capability under high temperature has been recently established and designated CRISPR/Cas12b (C2c1). Cas12b has also shown temperature induci...
Article
Full-text available
Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR-Cas system has led to significant progress in the field of plant and animal breeding. The CRISPR-Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter d...
Article
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Cotton (Gossypium hirsutum) is an important fiber crop worldwide. Insect attack causes cotton yield and quality losses. However, little is known about the mechanism of cotton response to insect attack. We simulated insect feeding by applying insect oral secretions (OS) to wounds, and combined transcriptome and metabolome analysis to investigate how...
Article
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The base‐editing technique using CRISPR/nCas9 (Cas9 nickase) or dCas9 (deactivated Cas9) fused with cytidine deaminase is a powerful tool to create point mutations. In this study, a novel G. hirsutum‐Base Editor 3 (GhBE3) base editing system has been developed to create single base mutations in the allotetraploid genome of cotton (Gossypium hirsutu...
Article
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As an allotetraploid, most genes have multiple copies that belong to At and Dt subgenomes in cotton. Different types of gene editing tools are desirable for the functional genomic research in cotton: a plant species with very complex genome (AADD, 2n=4x=52; genome size of 2.5 Gb). CRISPR/Cpf1 (Cas12a) is a novel member of CRISPR‐Cas system from Ali...
Article
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Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1–4. Here we report referencegrade genome assemblies and annotations for G. hirsutum accession Tex...
Data
Figure S1 CG, CHG and CHH methylation patterns of TEGs and PCGs. Figure S2 The numbers of hypomethylated (Hypo) and hypermethylated (Hyper) context‐specific differentially methylated regions (DMRs) in regenerated plants. Figure S3 A circos plot of the TE density, gene density, CG‐differentially methylated region (DMR), CHG‐DMR, and CHH‐DMR in com...
Data
Table S1 Summary of BS‐Seq data in G. hirsutum. Table S2 Identification of methylated cytosines in each of the seven samples. Table S3 Summary of small RNA‐Seq data. Table S4 Summary of H3K9me2 data. Table S5 Summary of the full names of DNA methylation pathway related genes. Table S6 Summary of RNA‐Seq data. Table S7 Summary of RNA‐Seq data...
Data
Data S2 The hyper‐DMRs (promoter 2‐kb) in ECs and corresponding gene expression from NEC to EC.
Data
Data S1 The expression and mCHH methylation encoding RdDM pathway genes.
Data
Data S3 The expression and mCHH methylation hormone‐related genes somatic embryogenesis process.
Article
Full-text available
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9‐edited plants. To identify on‐ and off‐target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9‐edited cotton plants targeted to three genes, and 3 negative (Ne) control and...
Article
Full-text available
Key message This research based on RNA-seq, biochemical, and cytological analyses sheds that ROS may serve as important signaling molecules of cytoplasmic male sterility in CMS-D8 cotton. Abstract To understand the mechanism of cytoplasmic male sterility in cotton (Gossypium hirsutum), transcriptomic, cytological, and biochemical analysis were per...
Article
Full-text available
Plant regeneration via somatic embryogenesis is time‐consuming and highly genotype‐dependent. The plant somatic embryogenesis process provokes many epigenetics changes including DNA methylation and histone modification. Recently, an elite cotton Jin668, with an extremely high regeneration ability, was developed from its maternal inbred Y668 cultiva...
Article
Full-text available
Genes encoding reporter proteins are used as visual marker-assisted tools in genetic transformation as well as plant breeding. In this study, the red fluorescent protein identified in Discosoma sp. coral (DsRed2) was successfully used as a visual marker for cotton genetic engineering. DsRed2 was successfully expressed in two cotton cultivars, JIN6...
Article
Full-text available
Plants have developed sophisticated systems to cope with herbivore challenge, including morphological barriers and secondary metabolites to reduce damage. In this study, 550 Gossypiumgenotypes were evaluated for whitefly(Bemisia tabaci) resistance in five experiments including two in thefield and three in the greenhouse, with 23 resistant and 19 su...
Article
Full-text available
Plants have developed sophisticated systems to cope with herbivore challenge, including morphological barriers and secondary metabolites to reduce damage. In this study, 550 Gossypium genotypes were evaluated for whitefly (Bemisia tabaci) resistance in five experiments including two in the field and three in the greenhouse, with 23 resistant and 19...
Article
Full-text available
Plants have developed sophisticated systems to cope with herbivore challenge, including morphological barriers and secondary metabolites to reduce damage. In this study, 550 Gossypiumgenotypes were evaluated for whitefly(Bemisia tabaci) resistance in five experiments including two in thefield and three in the greenhouse, with 23 resistant and 19 su...
Data
Figure S1 Cloning of AtU6‐26 homologous genes and their promoters in cotton. Figure S2 Modification of pGERB32 vector for cotton gene transformation. Figure S3 Procedure for pPTG vectors construction with one step cloning method. Figure S4 The DsRed2 transgenic cotton line RED has red fluorescence in all tissues. Figure S5 Designed PTG genes fo...
Article
Plants are constantly challenged by a multitude of pathogens and pests, which causes massive yield and quality losses annually. A promising approach to reduce such losses is to enhance the immune system of plants through genetic engineering. Previous work has shown that laccases (p-diphenol:dioxygen oxidoreductase, EC 1.10.3.2) function as lignin p...
Article
Plants are prone to a number of pathogens and abiotic stresses that cause various disorders. However, plants possess a defense mechanism to cope with these stresses. The osmotin protein belongs to the PR-5 family of Pathogenesis-related (PR) proteins, which are produced in response to diseases caused by various biotic and abiotic stresses. Osmotin...
Article
Insect sex pheromones (SPs) are central to mate-finding behaviour, and play an essential role in the survival and reproduction of organisms. Understanding the roles, biosynthetic pathways and evolution of insect chemical communication systems has been an exciting challenge for biologists. Compared with Lepidoptera, little is known about the mechani...
Article
Full-text available
Plant bugs (Miridae species), which are sap-sucking insects, have emerged as major pests of cotton in China. Most Miridae species are not sensitive to commercial Bacillus thuringiensis (Bt) cotton, resulting in significant economic losses and an increased application of insecticide, which eventually may compromise the future of Bt cotton. We demons...
Article
Full-text available
Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologs. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (Clustered Regularly Interspaced Sh...
Article
Full-text available
Many reports showed that polyamine oxidase (PAO) genes play crucial roles in various abiotic and biotic stresses response. In this study, 12 putative PAO genes (GhPAO1–GhPAO12) were identified in upland cotton (Gossypium hirsutum L.) genome using the released genome database. A total of 349 cis-acting factors involved in hormone and stress response...
Article
Full-text available
Comparative population genomics offers an excellent opportunity for unraveling the genetic history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an important economic crop, but a genome-wide and evolutionary understanding of the effects of human selection is lacking. Here, we describe a variation map for 352 wild and domes...
Article
Full-text available
The bZIP transcription factor (TF) act as an important regulator for the abscisic acid (ABA) mediated abiotic stresses signaling pathways in plants. Here, we reported the cloning and characterization of GhABF2, encoding for typical cotton bZIP TF. Overexpression of GhABF2 significantly improved drought and salt stress tolerance both in Arabidopsis...