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SapBase:A central portal for functional and comparative genomics of Sapindaceae species

Journal of Integrative Plant Biology 2024年第8期66卷 1561-1570页

作者： Jiawei Li Chengjie Chen zaohai zeng Fengqi Wu Junting Feng Bo Liu Yingxiao Mai Xinyi Chu Wanchun Wei Xin Li Yanyang Liang YuanLong Liu Jing Xu Rui Xia State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510640China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs South China Agricultural UniversityCollege of HorticultureGuangzhou 510640China

The Sapindaceae family,encompassing a wide range of plant forms such as herbs,vines,shrubs,and trees,is widely distributed across tropical and subtropical *** family includes economically important crops like litchi,longan,rambutan,and *** the wide application of genomic technologies in recent years,several Sapindaceae plant genomes have been decoded,leading to an accumulation of substantial omics data in this *** surge in data highlights the pressing need for a unified genomic data center capable of storing,sharing,and analyzing these ***,we introduced SapBase,that is,the Sapindaceae Genome *** houses seven published plant genomes alongside their corresponding gene structure and functional annotations,small RNA annotations,gene expression profiles,gene pathways,and synteny block *** offers user-friendly features for gene information mining,co-expression analysis,and interspecies comparative genomic ***,we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in ***,Sap Base could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.

关键词： functional crops unified

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Small RNAs, emerging regulators critical for the development of horticultural traits

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Horticulture Research 2018年第1期5卷 285-298页

作者： Chengjie Chen zaohai zeng Zongrang Liu Rui Xia State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhou510642China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China Ministry of AgricultureSouth China Agricultural UniversityGuangzhou510642China Guangdong Litchi Engineering Research Center College of HorticultureSouth China Agricultural UniversityGuangzhou510642China Appalachian Fruit Research Station Agricultural Research ServiceUnited States Department of AgricultureKearneysvilleWV25430USA

Small RNAs(sRNAs)have been recently recognized as key genetic and epigenetic regulators in various organisms,ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding *** plants,major regulatory sRNAs are classified as respective microRNA(miRNA)and small interfering RNA(siRNA)species,with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional *** of these characterized sRNAs are involved in regulation of diverse biological programs,processes,and pathways in response to developmental cues,environmental signals/stresses,pathogen infection,and pest ***,sRNAs-mediated regulations have also been extensively investigated in horticultural plants,with many novel mechanisms unveiled,which display far more mechanistic complexity and unique regulatory features compared to those studied in model ***,we review the recent progress of sRNA research in horticultural plants,with emphasis on mechanistic aspects as well as their relevance to trait *** that major and pioneered sRNA research has been carried out in the model and other plants,we also discuss ongoing sRNA research on these *** miRNAs and phased siRNAs(phasiRNAs)are the most studied sRNA regulators,this review focuses on their biogenesis,conservation,function,and targeted genes and traits as well as the mechanistic relation between them,aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops.

关键词： Small critical latter

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Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in Dimocarpus longan Lour.

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Horticultural Plant Journal 2023年第2期9卷 237-249页

作者： Bo Liu Guanliang Li Chengjie Chen zaohai zeng Jing Xu Jisen Zhang Rui Xia Yuanlong Liu State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhouGuangdong 510640China Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhouGuangdong 510640China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouGuangdong 510640China Center for Genomics and Biotechnology Haixia Institute of Science and TechnologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouFujian 350002China

Flower development plays vital role in horticultural ***-transcriptional regulation via small RNAs is important for plant flower *** uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house *** results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive ***-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and ***482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from *** small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.

关键词： Dimocarpus longan Lour Small RNAs Flower development Post-transcriptional regulation

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

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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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