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Plant genomic resources at National genomics Data Center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the National genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng Agricultural genomics Institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw *** advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea ***,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress ***,a considerable gap remains between pea functional genomics and molecular *** review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

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World Journal of Gastroenterology 2025年第3期31卷 84-102页

作者： Patricia de la Cruz-Ojeda Ester Parras-Martínez Raquel Rey-Pérez Jordi Muntané Functional genomics of Solid Tumors Laboratory Centre de Recherche des CordeliersParis 75006France Department of Oncology Surgery Cell Therapy and Organ TransplantationInstitute of Biomedicine of SevilleVirgen del Rocio University HospitalSeville 41013Spain Biomedical Research Center for Hepatic and Digestive Diseases CIBERehdMadrid 28029Spain Department of Medical Physiology and Biophysics University of SevilleSeville 41009Spain

BACKGROUND Hepatocellular carcinoma(HCC)is the most common subtype of primary liver cancer with varied incidence and epidemiology *** is still a recommended treatment for a large proportion of patients with advanced *** patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 *** To define the long non-codingRNA-microRNA-mRNA(lncRNA-miRNA-mRNA)predicted signatures related to selected hallmarks of cancer(apoptosis,autophagy,cell stress,cell dedifferentiation and invasiveness)in RNAseq studies using Sorafenib-treated HepG2 and SNU449 *** available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 *** HepG2 and SNU449 cells were treated with Sorafenib(10μmol/L)for 24 *** RNA,including small and long RNA,was extracted with a commercial miRNeasy *** was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory *** MALAT,THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7,TIRARP,TFAP4 and FAXDC2 in HepG2 ***12,EPB41 L4A-AS1,LINC01578,SNHG12 and GAS5 interacted with let-7b-3p,miR-195-5p and VEGFA in SNU449 *** axes MALAT1/hsamir-374b-3p/SMAD7 and MALAT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells,whereas PVT1/hsa-miR-195-5p/VEGFA was responsible for the differential response of SNU449 cells to Sorafenib *** Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression,whose proteins mainly increased the antitumor effectiveness of the treatment(SMAD7,TIRARP,TFAP4,FAXDC2 and ADRB2).However,the broad regulatory axis leading to increased VEGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

关键词： Cell culture Hepatocellular carcinoma Non-coding RNA RNAseq Sorafenib

An online coronavirus analysis platform from the National genomics Data Center

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Zoological Research 2020年第6期41卷 705-708页

作者： Zheng Gong Jun-Wei Zhu Cui-Ping Li Shuai Jiang Li-Na Ma Bi-Xia Tang Dong Zou Mei-Li Chen Yu-Bin Sun Shu-Hui Song Zhang Zhang Jing-Fa Xiao Yong-Biao Xue Yi-Ming Bao Zheng-Lin Du Wen-Ming Zhao China National Center for Bioinformation&National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions *** continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.

关键词： acute respiratory continued

Rice genomics: over the Past Two Decades and into the Future

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genomics, Proteomics & Bioinformatics 2018年第6期16卷 397-404页

作者： Shuhui Song Dongmei Tian Zhang Zhang Songnian Hu Jun Yu BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

关键词： Rice genome Genomic diversity Heterosis Domestication

Being the Pioneer of Life Sciences in China——Introduction to Beijing genomics Institute

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genomics, Proteomics & Bioinformatics 2004年第1期2卷 59-63页

作者： Xin Zhang Beijing genomics Institute, Beijing 101300, China. Beijing genomics Institute Beijing 101300 China

The Beijing genomics Institute (BGI) of Chinese Academy of Sciences (CAS) wasofficially founded in December 2003. Its predecessor, Beijing Huada genomics Research Center, haspresented significant contributions to the development of life sciences in China by its excellentscientific innovations and achievements in the last five years. From the participation ofInternational Human Genome Project (HGP) to the independent completion of the whole-genome draft andfine maps of Chinese super hybrid rice genome, from the porcine genome research cooperated withDenmark to the international chicken genome research, and from the silkworm genome projectaccomplished together with The Southwest Agriculture University of China to the great contributionsto the national campaign against SARS, all these facts illustrate that BGI not only has afirst-class scientific research power in the world but also is full of devotion to the flourish ofscience and nation. During these years, we have upheld the strategy of ''Advance through projects,strive for innovation, grow through cooperation'', in the aim of making BGI as one of the pioneers ofCAS climbing the peak of life sciences in the world.

关键词： Chinese Academy of Sciences Beijing genomics Institute innovation life sciences

Toward A New Paradigm of genomics Research——Celebration of the 20th Anniversary of Beijing Institute of genomics

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genomics, Proteomics & Bioinformatics 2023年第5期21卷 904-909页

作者： Zhang Zhang Songnian Hu Jun Yu National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Twenty years after the completion and forty years after the proposal of the Human Genome Project(HGP),genomics,together with its twin field-bioinformatics,has entered a new paradigm,where its bioscience-related,discipline-centric applications have been creating many new research *** Institute of genomics(BIG),now also known as China National Center for Bioinformation(CNCB),will play key roles in supporting and participating in these frontier research *** the 20th anniversary of the establishment of BIG,we provide a brief retrospective of its historic events and ascertain strategic research directions with a broader vision for future genomics,where digital genome,digital medicine,and digital health are so structured to meet the needs of human life and healthcare,as well as their related metaverses.

关键词： genomics Bioinformatics BIG CNCB NGDC

Small RNA in rice genome

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Science China(Life Sciences) 2002年第5期45卷 497-503页

作者：王凯朱小蓬钟兰陈润生 Beijing genomics Institute/Center of genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China College of Life Sciences Peking University Beijing 100871 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Laboratory of Bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.

关键词： ncRNA, sRNA, conserved sequences, plant-specific sRNA gene.

Development of a functional cell-based HTS assay for identification of NKCC1-negative modulators

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Chinese Science Bulletin 2014年第7期59卷 630-638页

作者： Yanqiu Bai Lianghui Ma Shiyou Li Beijing Institute of genomics Chinese Academy of Sciences University of Chinese Academy of Sciences Laboratory of Disease genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences

Na–K–Cl cotransporter 1(NKCC1) cotransports Na+, K+, and Cl-ions across the plasma membrane into cells. Accumulation of Cl-ions in dorsal root ganglion neurons induces depolarizing GABAA receptors, which mediate presynaptic inhibition and filtration of sensory noise. The activity of the Na–K–Cl cotransporter is modulated by high-dose loop diuretics, such as furosemide and bumetanide. To identify NKCC1 modulators, we developed a functional cell-based assay feasible for highthroughput screening(HTS), in which the activity of NKCC1 was detected by a BTC-AM dye-based thallium transportation assay. We demonstrated that the influx of Tl?was mediated by NKCC1, which required the existence of Cl-ions and could be inhibited by bumetanide and furosemide. Our results demonstrated that the assay was stable, reproducible, and suitable for HTS of negative modulators for NKCC1.

关键词：细胞膜测定法 HTS 调节剂识别背根神经节神经元 GABAA受体转运蛋白