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Shaken not stirred: A molecular contribution to the systematics of genus Mugil (Teleostei, Mugilidae)

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Integrative Zoology 2016年第4期11卷 263-281页

作者： Sandra HERAS Ferruccio MALTAGLIATI Maria Victoria FERNÁNDEZ María Inés ROLDÁN Laboratory of Genetic Ichthyology University of GironaGironaSpain Department of Biology University of PisaPisaItaly

With this work we addressed some molecular systematic issues within the Mugil cephalus species complex.Particular attention was paid to the debated situations of:(i)Mugil liza,occurring in partial sympatry with Mugil cephalus in the northwestern Atlantic,and(ii)Mugil platanus,considered by some authors a synonymy of the former species and distributed in the southwestern Atlantic.We sequenced 79 individuals of a 465-bp portion of the mitochondrial control region(CR)from 8 western Atlantic and 2 Mediterranean localities.In addition,all CR sequences available from GenBank for the studied taxa were added to our dataset,for a total of 323 individuals.Overall,229 haplotypes corresponding to 8 divergent monophyletic lineages were detected.Results of phylogenetic analyses were consistent with the occurrence of past speciation events producing the observed lineages.Of these lineages,7 correspond to cryptic species and one is constituted by M.liza and M.platanus.As a matter of fact,these 2 taxa constitute a single lineage within the M.cephalus species complex.However,individuals of M.liza/M.platanus lineage analyzed by means of the 18 mitochondrial markers available in GenBank exhibited a degree of genetic diversity consistent with highly divergent populations.Of the 8 lineages detected,the Mediterraean one(type locality)corresponds to M.cephalus;the lineage M.liza/M.platanus should be named M.liza,under the priority principle,and the left 6 lineages need formal description.

关键词： cryptic species historical demography molecular phylogeny Mugil systematics

Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat

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Plant Diversity 2024年第3期46卷 386-394页

作者： Yunzhen Li Liujie Jin Xinyu Liu Chao He Siteng Bi Sulaiman Saeed Wenhao Yan National Key laboratory of Crop genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Vernalization is necessary for winter wheat to flower.However,it is unclear whether vernalization is also required for spring wheat,which is frequently sown in fall,and what molecular mechanisms underlie the vernalization response in wheat varieties.In this study,we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties.For this purpose,we determined how major vernalization genes(VRN1,VRN2,and VRN3)respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression.We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties.We found that in winter wheat,but not in spring wheat,VRN1 expression decreases when returned to warm temperature following vernalization.This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3(H3K27me3)and tri-methylation of lysine 4 on histone H3(H3K4me3)at the VRN1 gene.Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes,including those involved in leucine catabolism,cysteine biosynthesis,and flavonoid biosynthesis.These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.

关键词： Wheat Vernalization VRN1 Histone modification Regulate network

Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importinβSAD2

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植物学报:英文版 2023年第9期65卷 2086-2106页

作者： Gang Chen Danyun Xu Qing Liu Zhichuang Yue Biao Dai Shujuan Pan Yongqiang Chen Xinhua Feng Honghong Hu National Key laboratory of Crop genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Flowering locus C(FLC)is a central transcriptional repressor that controls flowering time.However,how FLC is imported into the nucleus is unknown.Here,we report that Arabidopsis nucleoporins 62(NUP62),NUP58,and NUP54 composed NUP62-subcomplex modulates FLC nuclear import during floral transition in an importinα-independent manner,via direct interaction.NUP62 recruits FLC to the cytoplasmic filaments and imports it into the nucleus through the NUP62-subcomplex composed central channel.Importinβsupersensitive to ABA and drought 2(SAD2),a carrier protein,is critical for FLC nuclear import and flower transition,which facilitates FLC import into the nucleus mainly through the NUP62-subcomplex.Proteomics,RNAseq,and cell biological analyses indicate that the NUP62-subcomplex mainly mediates the nuclear import of cargos with unconventional nuclear localization sequences(NLSs),such as FLC.Our findings illustrate the mechanisms of the NUP62-subcomplex and SAD2 on FLC nuclear import process and floral transition,and provide insights into the role of NUP62-subcomplex and SAD2 in protein nucleocytoplasmic transport in plants.

关键词： FLC flowering time importin nuclear import nucleoporin

Composition and Function of Bacterial Communities of Bryophytes and Their Underlying Sediments in the Dajiuhu Peatland, Central China

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Journal of Earth Science 2023年第1期34卷 133-144页

作者： Xing Xiang Hongmei Wang Wen Tian Ruicheng Wang Linfeng Gong Ying Xu Baiying Man College of life science Shangrao Normal UniversityShangrao334001China State Key laboratory of Biogeology and Environmental Geology China University of GeosciencesWuhan430074China State Key laboratory Breeding Base of Marine genetic Resources Key Laboratory of Marine Genetic ResourcesThird Institute of OceanographySOAKey Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen361005China

Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosystems. To explore the differences in community structure, metabolic potential and interaction relationship of bacterial microbiomes associated with different bryophytes species, the gametophytes of three bryophyte species(Sphagnum palustre, Aulacomnium androgynum, and Polytrichum commune) and their underlying peat sediments were collected from the subtropical Dajiuhu Peatland and subjected to Illumina high-throughout sequencing of 16S r RNA gene. Results showed that bacterial diversity was lowest in S. palustre, the dominant moss species, among the three moss species investigated in Dajiuhu Peatland. Bacterial communities from bryophytes clearly separated with those from sediments as indicated by both phylogenetic and taxonomical approaches. Linear discriminant analysis effect size(LEf Se) identified 30 and 36 indicator taxa in mosses and peat sediments. Bacteroidetes, Verrucomicrobia and Thermoleophilia significantly enriched in S. palustre, A. androgynum and P. commune, Chloroflexi, Proteobacteria and Acidobacteria subgroup 6 was indicator taxa for corresponding underlying sediments, respectively. Despite of these differences in compositions, bacterial functional structures were similar among all bryophytes, such as abundant aerobic heterotrophs, rare nitrifiers and denitrifiers. This phenomenon was also observed among the underlying sediments. Network analysis indicated that Proteobacteria and Acidobacteria located in the center of network and exerted strong interactions to other taxa. The sub-network of bacterial communities in sediments was more connected and microbial groups were more competitive than those in bryophytes subnetwork. Our results offer new insight into the community structure, ecological function and interaction pattern of bacterial microbiomes in the Dajiuhu Peatland across diff

关键词： bryophytes bacteria bacterial microbiome indicator taxa co-occurrence network the Dajiuhu Peatland

Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

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Journal of Animal Science and Biotechnology 2022年第3期13卷 707-720页

作者： Zhongzi Wu Huanfa Gong Zhimin Zhou Tao Jiang Ziqi Lin Jing Li Shijun Xiao Bin Yang Lusheng Huang State Key laboratory for Pig genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchangChina

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDRgenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

关键词： Cis-eQTL Co-localization Gene expression Liver Pig heterogeneous population Short tandem repeats

CircRNA: a rising star in plant biology

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Journal of genetics and Genomics 2022年第12期49卷 1081-1092页

作者： Pei Zhang Mingqiu Dai National Key laboratory of Crop genetic Improvement Huazhong Agricultural UniversityWuhanHubei 430070China

Circular RNAs(circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding mi RNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and,particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue-or developmentspecific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circ RNA studies.

关键词： Plant circRNA circRNA biogenesis circRNA regulation Roles of circRNA Methodologies in circRNA studies

Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus

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Science China(Life Sciences) 2023年第11期66卷 2614-2628页

作者： Siyu Yang Dong Chen Lei Xie Xiaoxiao Zou Yanyuan Xiao Lin Rao Tianxiong Yao Qing Zhang Liping Cai Fei Huang Bin Yang Lusheng Huang State Key laboratory of Pig genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China

The hippocampus is a brain region associated with memory,learning and spatial navigation,its aging-related dysfunction is a common sign of Alzheimer’s disease.Pig is a good model for human neurodegenerative disease,but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited.Here,we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages.We identified 510,908 accessible chromatin regions(ACRs)in 12 major cell types,among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages.We revealed significant enrichment of transposable elements in cell type-specific ACRs,particularly in neuroblasts.We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development.We identified ACRs and key transcription factors underlying the trajectory of neurogenesis(such as POU3F3 and EGR1)and oligodendrocyte differentiation(RXRA and FOXO6).We examined 27 Alzheimer’s disease-related genes in our data and found that 15 showed cell type-specific activity(TREM2,RIN3 and CLU),and 15 genes displayed age-associated dynamic activity(BIN1,RABEP1 and APOE).We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types.The present study provides a single nucleusaccessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases.

关键词： hippocampus pig chromatin accessibility gene expression nuclei accessible chromatin regions development

genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2345-2362页

作者： Lei Xie Jiangtao Qin Lin Rao Dengshuai Cui Xi Tang Liqing Chen Shijun Xiao Zhiyan Zhang Lusheng Huang State Key laboratory for Pig genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China

Background As pre-cut and pre-packaged chilled meat becomes increasingly popular,integrating the carcasscutting process into the pig industry chain has become a trend.Identifying quantitative trait loci(QTLs)of pork cuts would facilitate the selection of pigs with a higher overall value.However,previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts,neglecting the investigation of QTLs influencing these traits.This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips.Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values(GEBVs)for pork cuts.Results We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes,respectively.Specifically,we found that HMGA1,VRTN and BMP2 were associated with body length and weight.Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones,VRTN primarily affects the number of vertebrates,and BMP2 primarily affects the length of vertebrae and the size of hind leg bones.The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population,divided by the square root of the trait’s heritability.The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693.Notably,ribs,boneless picnic shoulder,tenderloin,hind leg bones,and scapula bones exhibited prediction accuracies exceeding 0.600.Employing better models,increasing marker density through genotype imputation,and pre-selecting markers significantly improved the prediction accuracy of GEBVs.Conclusions We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes.These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection.Additionally,we have constructed the first reference populations for genomic sele

关键词： Carcass morphology traits Genomic selection Genotype imputation GWAS Pork cuts

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato