Xuan Li

Guangdong Medical College

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Qi Zhao

University of Tennessee Health Science Center

Xueting Zhong

Capital Normal University

Li Qin Zhang

Huzhou University

Chou Fei Wu

Huzhou University

Zhanqi Wang

China University of Geosciences

Shaoguo Ru

Ocean University of China

Jun Wang

Cangzhou Normal University

Zhongshan Zhang

Huzhou University

Wei Fan

Zhengzhou University

Yang Tian

Tongji University

Cooperative Institutions

Chinese Academy of Sciences

141

University of Chinese Academy of Sciences

Ocean University of China

Chinese Academy of Agricultural Sciences

Ministry of Agriculture and Rural Affairs

Sun Yat-sen University

System Equipment (China)

Zhejiang University

Shanghai Jiao Tong University

Sichuan University

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Coprinus comatus: A basidiomycete fungus forms novel spiny structures and infects nematode

Mycologia (2004)

Hong Luo Ming‐He Mo Xiaowei Huang Xuan Li Ke‐Qin Zhang

Nematophagous basidiomycete fungi kill nematodes by trapping, endoparasitizing and producing toxin. In our studies Coprinus comatus (O.F.Müll. : Fr.) Pers. is found to be a nematode-destroying fungus; this fungus immobilizes, kills and uses free-living nematode Panagrellus redivivus Goodey and root-knot nematode Meloidogyne arenaria Neal. C. comatus produces an unusual structure designated spiny ball. Set on a sporophore-like branch, the spiny ball is a burr-like structure assembled with a large number of tiny tubes. Purified spiny balls exhibit moderate nematicidal activity. Experiments show that spiny balls are not chlamydospores because of the absence of nuclei in the structures and quick formation within 3 d in a young colony. Nematodes added to C. comatus cultures on potato-dextrose agar (PDA) and cornmeal agar (CMA) become inactive in hours. Infection of nematodes by the fungus occurs only after the nematodes are immobilized (feeble or dead), probably by a toxin. Electron micrographs illustrate that C. comatus infect P. redivivus by producing penetration pegs with which hyphae colonize nematode bodies. An infected nematode is digested and consumed within days and hyphae grow out of the nematode.

Root-knot nematode

10.1080/15572536.2005.11832870

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Citations (75)

ICN 2023 TOC

Fangyong Peng Yang Yan Dong Lin Song Xijin Wei‐Ting Wu

10.1109/icn60549.2023.10426501

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Development of a Melting Curve-Based Triple Eva Green Real-Time PCR Assay for Simultaneous Detection of Three Shrimp Pathogens

Animals (2024)

Xuan Dong Yujin Chen Haoyu Lou Guohao Wang Chengyan Zhou

Infections with Enterocytozoon hepatopenaei (EHP), infectious hypodermal and hematopoietic necrosis virus (IHHNV), and Decapod iridescent virus 1 (DIV1) pose significant challenges to the shrimp industry. Here, a melting curve-based triple real-time PCR assay based on the fluorescent dye Eva Green was established for the simultaneous detection of EHP, IHHNV, and DIV1. The assay showed high specificity, sensitivity, and reproducibility. A total of 190 clinical samples from Shandong, Jiangsu, Sichuan, Guangdong, and Hainan provinces in China were evaluated by the triple Eva Green real-time PCR assay. The positive rates of EHP, IHHNV, and DIV1 were 10.5%, 18.9%, and 44.2%, respectively. The samples were also evaluated by TaqMan qPCR assays for EHP, DIV1, and IHHNV, and the concordance rate was 100%. This illustrated that the newly developed triple Eva Green real-time PCR assay can provide an accurate method for the simultaneous detection of three shrimp pathogens.

TaqMan

Melting curve analysis

10.3390/ani14040592

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A chromosome conformation capture ordered sequence of the barley genome

Nature (2017)

Martin Mascher Heidrun Gundlach Axel Himmelbach Sebastian Beier Sven Twardziok

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare. Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley (Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.

Triticeae

Lineage (genetic)

Germ plasm

Sequence (biology)

Genomic Organization

10.1038/nature22043

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Citations (1,317)

A case of polyploid utility in biocontrol: reproductively‐impaired triploid Nasonia vitripennis have high host‐killing ability

Pest Management Science (2024)

Xuan Li Kelley Leung

Intentionally impairing the fecundity of mass-reared insects has important utility in controlling pest species. Typically, sterilized individuals are competed against wild counterparts, reducing pest population size. A novel consideration is creating biocontrol agents with lower reproductive capacity that are less likely to establish permanently or admix with wild populations, which are both emerging as legal barriers. Hymenopterans have diploid females, but archetypically infertile polyploid triploid females occur for various parasitoid species. As a first test of polyploid utility for these biocontrol concerns, we assessed the species with the best characterized polyploid biology, the gregarious idiobiont Nasonia vitripennis, for triploid female host-killing ability on pupal blowfly hosts (Calliphora vomitoria).

Polyploid

Nasonia vitripennis

10.1002/ps.8548

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A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis)

Marine Biotechnology (2019)

Zujing Yang Xuan Li Huan Liao Liping Hu Cheng Peng

Patinopecten yessoensis

SNP

Fosmid

10.1007/s10126-019-09918-6

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Citations (7)

Additional file 1: Table S1. of Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius)

Figshare (2015)

Huaan Yang Jianbo Jian Xuan Li Daniel Renshaw Jon Clements

Genotyping of sequence-defined SNP markers and InDel markers from the genetic linkage map [38] on 10 commercial cultivars through genome sequencing and re-sequencing in Lupinus angustifolius. (XLSX 475 kb)

10.6084/m9.figshare.c.3609371_d3

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Studies on distribution and population of amphioxus(Branchiostoma belcheri) in Maoming Dafangji sea area

Zhongguo shengtai nongye xuebao (2007)

Xuan Li

The investigation indicates that amphioxus (Branchiostoma belcheri) is mainly distributed within the area with 111°10′～111°17′longitude, 21°19′～21°27′latitude, which covers 195.5km2 in Maoming Dafangji sea areas. The average resource density is 51～86 ind/m2, the highest is 815 ind/m2. The area with a high density is centered in the west and northwest of the Xiaofangji Island. The body length distribution of amphioxus has an obvious seasonal fluctuation and the main recruit seasons are autumn and winter. The gonad maturity and sex ratio of population significantly change with seasons and growth stages and with a highest proportion of sex mature 65% in spring. Furthermore, along with the increase of the body length ,the gonad maturity is increased gradually. Gonad maturity percentage is a function of binary cubic curve to the body length. Within the scope of 35～60mm of body length, the sex ratio of population approaches 1; if the body length is longer than 60mm the individuals of female are obviously less than those of male; the body length-weight relation equation of amphioxus is W = 0.0012L3.32. As the body length is longer than 50mm, the reducing coefficient of amphioxus population is 0.55/cm.

Longitude

Population density

Density dependence

Source

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An Integrated Genetic and Cytogenetic Map for Zhikong Scallop, Chlamys farreri, Based on Microsatellite Markers

PLoS ONE (2014)

Liying Feng Liping Hu Xiaoteng Fu Huan Liao Xuan Li

The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species.

Genetic linkage

Linkage (software)

10.1371/journal.pone.0092567

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Citations (12)

[Up-regulation of major histocompatibility complex class I-related molecules A (MICA) induced by 5-aza-2'-deoxycytidine].

Jinfeng Wu Gui-Li Zeng Wei Shen Mei Yang Feng Wang

Major histocompatibility complex class I C-related molecules A and B (MICA and MICB) are innate immune system ligands for the NKG2D receptor expressed by natural killer cells and activated CD8(+)T cells. Our previous study showed that 5-aza-2'-deoxycytidine (5-aza-dC), a DNA methyltransferase inhibitor, can induce the expression of MICB and sensitized cells to NKL-cell-mediated cytolysis. The aim of this study was to determine the expression level of MICA in HepG2 cells (an HCC cell line) and L02 cells ( a normal liver cell), and to investigate the effect of 5-aza-dC on MICA expression in HepG2 cells.Cells were treated with 5-aza-dC, caffeine and ATM-specific siRNA. The cell surface MICA protein on HepG2 cells and L02 cells was determined using flow cytometry. The mRNA level was detected using real time RT-PCR.MICA was undetectable on the surface of L02 cells, but was highly expressed on HepG2 cells. MICA expression was upregulated in response to 5-aza-dC treatment (P less than 0.05), and the upregulation of MICA was partially prevented by pharmacological or genetic inhibition of ataxia telangiectasia mutated (ATM) kinase (P less than 0.05).Our data suggest that 5-aza-dC induces the expression of MICA by a DNA damage-dependent mechanism.

NKG2D

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Citations (2)