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TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

Molecular Plant 2023年第11期16卷 1733-1742页

作者： Chengjie Chen Ya Wu Jiawei Li Xiao Wang Zaohai Zeng Jing Xu Yuanlong Liu Junting Feng Hao Chen Yehua He Rui Xia State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510640China key laboratory of biology and Germplasm Enhancement of Horticultural crops in South China Ministry of Agriculture and Rural AffairSouth China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong key laboratory of Non-human Primate research Guangdong-Hongkong-Macao Institute of CNS RegenerationJinan UniversityGuangzhouGuangdong 510632China State key laboratory of Crop Stress Adaptation and Improvement Henan Joint International Laboratory for Crop Multi-Omics ResearchSchool of Life SciencesHenan UniversityKaifeng 475004China key laboratory of Genetic Improvement of Bananas Sanya Research InstituteState Key Laboratory of Tropical Crop BreedingInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China College of Agronomy Hunan Agricultural UniversityChangsha 410128China

Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic ***,TBtools is a commonly used tool in biological *** the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—*** this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data ***,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual *** date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools *** plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data ***,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and *** promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.

关键词： TBtools-ll plugin biological big data BSA-seq

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In tegrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patter ns of key metabolites associated with oil quality during seed ripening of Camellia oleifera

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Horticulture research 2021年第1期8卷 1997-2022页

作者： Zhouchen Ye Jing Yu Wuping Yan Junfeng Zhang Dongmei Yang Guanglong Yao Zijin Liu Yougen Wu Xilin Hou College of Horticulture Hainan UniversityHaikouChina State key laboratory of Crop Genetics&Germplasm Enhancement Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(East China)Ministry of Agriculture and Rural Affairs of the P.R.ChinaEngineering Research Center of Germplasm Enhancement and Utilization of Horticultural CropsMinistry of Education of the P.R.ChinaInstitute of Plasma EngineeringNanjingChina

Camellia oleifera(***)is one of the four major woody oil-bearing crops in the world and has relatively high ecological,economic,and medicinal *** seeds undergo a series of complex physiological and biochemical changes during ripening,which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality,especially flavonoids and fatty *** obtain new insights into the underlying molecular mechanisms,a parallel analysis of the transcriptome and proteome profiles of *** seeds at different maturity levels was conducted using RNA sequencing(RNA-seq)and isobaric tags for relative and absolute quantification(iTRAQ)complemented with gas chromatography-mass spectrometry(GC-MS)data.A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental *** these,317 were coexpressed with a poor correlation,and most were involved in metabolic processes,including fatty acid metabolism,a-linolenic acid metabolism,and glutathione *** addition,the content of total flavonoids decreased gradually with seed maturity,and the levels of fatty acids generally peaked at the fat accumulation stage;these results basically agreed with the regulation patterns of genes or proteins in the corresponding *** expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase(PAL)and chalcone synthase(CHS)as well as their cognate transcripts were positively correlated with the variation in the flavonoid content,while shikimate O-hydroxycinnamoyltransferase(HCT)-(encoding genes had the opposite *** increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase(ADH)was associated with a reduction in linoleic acid *** weighted gene coexpression network analysis(WGCNA),we further identi fied six unique modules related to flavonoid,oil,and fa

关键词： metabolism analysis maturity

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Genetic Analysis of Weight per Fruit and Fruit Length in Bitter Gourd

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Plant Diseases and Pests 2022年第5期13卷 25-27页

作者： Ziji LIU Yu NIU Yan YANG Baibi ZHU tropical crops Genetic Resources institute Chinese Academy of Tropical Agricultural SciencesHaikou 571011China hainan key laboratory of Vegetable biology Vegetable Research InstituteHainan Academy of Agricultural SciencesHaikou 571199China

[Objectives]The paper was to verify the genetic mechanism of weight per fruit and fruit length in bitter gourd and to provide guidance for formulating breeding strategy.[Methods]In this study,a cross was made between CN19-1 and Thai4-6,and a Fsegregation population was also *** genetic characteristics of weight per fruit and fruit length were analyzed by employing major gene plus polygene mixed genetic model.[Results]The weight per fruit and fruit length showed continuous distribution in Fsegregation *** optimal model for weight per fruit and fruit length was the same(A-1 model).The major gene additive effect value of weight per fruit was 46.1474,the dominant effect value was-46.1005,and the major gene heritability was 52.47%.The major gene additive effect value of fruit length was 2.456,the dominant effect value was-2.455,and the major gene heritability was 52.52%.The results showed that weight per fruit and fruit length were mainly controlled by a pair of major genes.[Conclusions]This study can provide a theoretical basis for bitter gourd breeding.

关键词： Bitter gourd Genetic model Weight per fruit Fruit length Genetic analysis

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Banana somatic embryogenesis and biotechnological application

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tropical Plants 2022年第1期1卷 96-108页

作者： Jingyi Wang Shanshan Gan Yunke Zheng Zhiqiang Jin Yunjiang Cheng Juhua Liu key laboratory of biology and Genetic Resources of tropical crops Ministry of AgricultureInstitute of Tropical Bioscience and Biotechnology/Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural Resources/Sanya Research InstituteChinese Academy of Tropical Agricultural Sciences(CATAS)Haikou 571101China key laboratory of Horticultural Plant biology(Ministry of Education) College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China

As one of the most important economic crops for both staple food and fruit widely cultivated in the tropics and subtropics,banana(Musa spp.)is susceptible to a plethora of abiotic and biotic *** cultivars resistant to abiotic and biotic stressors without adverse effects on yield and fruit quality are the objectives of banana improvement ***,conventional breeding approaches are time-consuming and severely hampered by inherent banana problems(polyploidy and sterility).Therefore,genetic transformation is becoming increasingly popular and can provide rapid *** efforts have been made to develop superior banana cultivars with better resistance to abiotic and biotic stresses and optimum yields using genetic modification *** embryogenesis(SE)through embryogenic cell suspension(ECS)cultures is an ideal recipient system for genetic transformation in *** purpose of this paper is to review the current status of banana somatic embryo research,clarify the process of banana somatic embryo induction and culture,and summarize the main influencing factors in the process of somatic *** the same time,their applications in breeding technologies such as cryopreservation,protoplast culture,genetic transformation and gene editing were also summarized,in order to provide reference for the research and practical application of banana somatic embryogenesis in the future.

关键词： breeding cultivar crops

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Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

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Horticulture research 2021年第1期8卷 181-194页

作者： Zhiqiang Xia Dongmei Huang Shengkui Zhang Wenquan Wang Funing Ma Bin Wu Yi Xu Bingqiang Xu Di Chen Meiling Zou Huanyu Xu Xincheng Zhou Rulin Zhan Shun Song Haikou Experimental Station Chinese Academy of Tropical Agricultural SciencesKey Laboratory of Genetic Improvement of Bananas571101 HaikouHainanP.R.China hainan University 571101 HaikouHainanP.R.China State key laboratory of Biobased Material and Green Papermaking Qilu University of Technology(Shandong Academy of Sciences)250353 JinanShandongP.R.China The institute of tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences571101 HaikouHainanP.R.China

Passion fruit(Passiflora edulis Sims)is an economically valuable fruit that is cultivated in tropical and subtropical regions of the ***,we report an~1341.7Mb chromosome-scale genome assembly of passion fruit,with 98.91%(~1327.18Mb)of the assembly assigned to nine *** genome includes 23,171 protein-coding genes,and most of the assembled sequences are repetitive sequences,with long-terminal repeats(LTRs)being the most *** analysis revealed that passion fruit diverged after Brassicaceae and before *** analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA,which may have contributed to its large genome *** integrated analysis of genomic,transcriptomic,and metabolomic data showed that‘alpha-linolenic acid metabolism’,‘metabolic pathways’,and‘secondary metabolic pathways’were the main pathways involved in the synthesis of important volatile organic compounds(VOCs)in passion fruit,and this analysis identified some candidate genes,including GDP-fucose Transporter 1-like,Tetratricopeptide repeat protein 33,protein NETWORKED 4B isoform X1,and Golgin Subfamily A member 6-like protein *** addition,we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene *** family analysis showed that the ACX,ADH,ALDH,and HPL gene families,especially ACX13/14/15/20,ADH13/26/33,ALDH1/4/21,and HPL4/6,were the key genes for ester synthesis,while the TPS gene family,especially PeTPS2/3/4/24,was the key gene family for terpene *** work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

关键词： metabolism synthesis insight

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Screening of Bitter Gourd Hybrid Combinations with High Yield and Disease Resistance

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Agricultural Biotechnology 2022年第4期11卷 40-42页

作者： Baibi ZHU Yu NIU Yan YANG Huang HE Ziji LIU hainan key laboratory of Vegetable biology Vegetable Research InstituteHainan Academy of Agricultural SciencesHaikou 571100China tropical crops Genetic Resources institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

[Objectives]This study was conducted to breed and promote high-yield and disease-resistant varieties of bitter gourd.[Methods]The comparison experiments of six new hybrid combinations(Z1705,Z1706,Z1717,Z1721,Z1732,Z1745)were successively carried out at two experimental sites of Danzhou and Tunchang.[Results]Comparing the agronomic traits and disease resistance of various combinations,it was concluded that Z1717 and Z1721 have high yields,green and glossy fruit surface and good comprehensive disease resistance,so they can be popularized and planted.[Conclusions]This study is of great significance for improving the yield of bitter gourd and increasing economic benefits.

关键词： Bitter gourd Fusarium wilt Powdery mildew Hybrid combination

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Genetic Analysis of Leaf Length and Leaf Width in Bitter Gourd

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Medicinal Plant 2022年第6期13卷 78-80页

作者： Ziji LIU Yu NIU Yan YANG Baibi ZHU tropical crops Genetic Resources institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China hainan key laboratory of Vegetable biology Vegetable Research InstituteHainan Academy of Agricultural SciencesHaikou 571101China

[Objectives]To explore the genetic mechanism that leaf length and leaf width in bitter gourd has realistic guiding significance for formulating breeding strategy.[Methods]In this paper,the cross was made between CN19-1 and Thai4-6 and an F2segregation population was *** genetic characteristics of leaf length and leaf width were analyzed by employing the major gene plus polygene mixed genetic model.[Results]The data analysis results demonstrated that the leaf length and leaf width of the F_(2) segregation population showed continuous *** optimum model for leaf length genetic analysis was A-1,the additive effect value of the major gene was 3.1766,the dominant effect value was-3.1766,and the heritability was 74.51%.The optimum model for leaf width genetic analysis was *** additive effect values of 2 pairs of major genes controlling the leaf width were 3.1917 and 0.9623,*** dominant effect values were-1.3135 and-0.3463,*** additive×additive interaction effect was-0.3591,the additive×dominant interaction effect was-0.2570,the dominant×additive interaction effect was 1.9916,the dominant×dominant interaction effect was *** heritability of major genes was 96.67%.[Conclusions]This study is expected to provide a theoretical basis for the breeding of bitter gourd.

关键词： Bitter gourd Genetic model Leaf length Leaf width Genetic analysis

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Identification and functional analysis of transcription factors related to coconut(Cocos nucifera L.)endosperm development based on ATAC-seq

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tropical Plants 2022年第1期1卷 62-72页

作者： Li Gao Yaning Wang Qinghui Guo Dongdong Li Sanya Nanfan research institute College of Tropical CropsHainan UniversityHainan 570228China

coconut(Cocos nucifera L.)is a member of the palm tree family(Arecaceae)and the only living species of the genus *** this paper,the regulatory relationship pathways between multiple transcription factors and functional genes were identified by combining ATAC-seq and RNAseq in coconut endosperm at four different developmental stages(fruit after pollination:7 months,8 months,9 months and 10 months,respectively).The results indicated that the peaks detected in the promoter-TSS area accounted for the largest proportion(11.99%)in the third *** results suggest that the chromatin open region of cells in this period is more functional and that there are more functional genes with active *** addition,a large number of potential regulatory relationships between transcription factors and functional genes were detected via bioinformatics analysis at the genomic *** them,CnGATA20 was predicted to be an important transcription factor with a binding site on the promoter region of the CnOLE18 *** regulatory pathway by which CnGATA20 positively regulates the expression of CnOLE18 was further confirmed by yeast one-hybrid,protoplast transient expression and dual-luciferase reporter system *** results provide a new research strategy for exploring the regulation at both the transcriptional and posttranscriptional levels during coconut endosperm growth and development.

关键词： functional analysis Co

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Genome wide identification and characterization of MAPK genes reveals their potential in enhancing drought and salt stress tolerance in Gossypium hirsutum

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Journal of Cotton research 2022年第3期5卷 261-273页

作者： SADAU Salisu Bello MEHARI Teame Gereziher AHMAD Adeel TAJO Sani Muhammad IBRAHIM Sani IQBAL Muhammad Shahid ELASAD Mohammed ZHANG Jingjing WEI Hengling YU Shuxun State key laboratory of Cotton biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China key laboratory of biology and Genetic Improvement of oil crops Ministry of AgricultureOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhan 430062China Department of Science and Technology Education Bayero University KanoP.O.Box 3011KanoNigeria Agricultural research Corporation(ARC) P.O.Box 126Wad MedaniSudan.

Background:The cotton crop is universally considered as protein and edible oil source besides the major contributor of natural fiber and is grown in tropical and subtropical regions around the world Unpredicted environmental stresses are becoming significant threats to sustainable cotton production,ultimately leading to a substantial irreversible economic ***-activated protein kinase(MAPK)is generally considered essential for recognizing environmental stresses through phosphorylating downstream signal pathways and plays a vital role in numerous biological ***:We have identified 74 MAPK genes across cotton,41 from ***,19 from ***,whereas 14 have been identified from *** MAPK gene-proteins have been further studied to determine their physicochemical characteristics and other essential *** this perspective,characterization,phylogenetic relationship,chromosomal mapping,gene motif,cis-regulatory element,and subcellular localization were carried *** on phylogenetic analysis,the MAPK family in cotton is usually categorized as A,B,C,D,and E *** to the results of the phylogenic relationship,cotton has more MAPKS genes in Clade A than Clade *** cis-elements identified were classified into five groups(hormone responsiveness,light responsiveness,stress responsiveness,cellular development,and binding site).The prevalence of such elements across the promoter region of these genes signifies their role in the growth and development of *** GHMAPK genes(GH_A07G1527,GH_D02G1138,GH_D03G0121,GH_D03G1517,GH_D05G1003,GH_D11G0040,and GH_D12G2528)were selected,and specific tissue expression and profiling were performed across drought and salt *** expressed that six genes were upregulated under drought treatment except for GH_D11G0040 which is *** all the seven genes have been upregulated at various hours of salt stress ***:RNA sequence and qPCR results showe

关键词： Cotton MAPK gene Drought stress Salt stress

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research Progress of Main Pests in Sweetsop ( Annona squamosa L. ) and Its Insecticide Activity

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Plant Diseases and Pests 2012年第5期3卷 1-3,10页

作者： Weicai LI Jianghui XIE Shengyou SHI Liqin LIU Yicheng WANG Yongzan WEI key laboratory of tropical Fruit biology ( Ministry of Agriculture) South Subtropical Crops Research InstituteCATAS

The research progress on pests and insecticide activity of Annona squamosa L. is summarized in the paper, including symptom, occurrence regularity and control methods. Furthermore, the comprehensive technique for cont... 详细信息

关键词： Annona squamosa L. Pest Control Insecticidal activity

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