首页期刊导航|基因组蛋白质组与生物信息学报（英文版）
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基因组蛋白质组与生物信息学报（英文版）
基因组蛋白质组与生物信息学报（英文版）

杨焕明；于军

双月刊

1672-0229

journal@cspg.net

010-84097425

100101

北京市朝阳区北辰西路1-7号中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报（英文版）/Journal Genomics、Proteomics & BioinformaticsCSCDCSTPCD北大核心SCI
查看更多>>Genomics, Proteomics & Bioinformatics (《基因组蛋白质组与生物信息学报》，简称GPB)创刊于2003年，是由中国科学院北京基因组研究所主办、科学出版社出版的国家级英文学术期刊，由杨焕明教授、于军教授担任主编，汪建教授、贺福初院士担任副主编。 本刊主要刊载基因组学、蛋白质组学、生物信息学及其相关领域的研究进展、综述、研究论文、实验技术与方法、研究快讯等高质量的稿件，突出刊物的学术性、前沿性、指导性和实用性。 本刊读者对象为基础医学、生命科学、农学、计算机科学领域的科研与教学人员、研究生等，以及数学、物理学领域对生物科学有兴趣的研究者。 GPB (ISSN 1672-0229，CN11-4926/Q)现为季刊，面向国内外发行，邮发代号80-113。2004年国内定价每期45元，全年180元。 欢迎赐稿和订阅! 联系人：张欣 《基因组蛋白质组与生物信息学报》编辑部 北京空港科技创业园B区6号 101300 Tel: 010-80485179 Fax: 010-80498676 E-mail：editor@genomics.org.cn Http：
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    Recent Advances in Assembly of Complex Plant Genomes

    Weilong KongYibin WangShengcheng ZhangJiaxin Yu...
    427-439页
    查看更多>>摘要：Over the past 20 years,tremendous advances in sequencing technologies and computa-tional algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of nonvascular plants to those of flowering plants.However,complex plant genome assembly is still challenging and remains difficult to fully resolve with conven-tional sequencing and assembly methods due to high heterozygosity,highly repetitive sequences,or high ploidy characteristics of complex genomes.Herein,we summarize the challenges of and advances in complex plant genome assembly,including feasible experimental strategies,upgrades to sequencing technology,existing assembly methods,and different phasing algorithms.Moreover,we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes.Finally,we expect that the accurate,gapless,telomere-to-telomere,and fully phased assembly of complex plant genomes could soon become routine.
      原文链接:
    • 万方数据
    • 维普

    A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

    Le WangMay LeeZi Yi WanBin Bai...
    440-454页
    查看更多>>摘要：The palm family(Arecaceae),consisting of～2600 species,is the third most economically important family of plants.The African oil palm(Elaeis guineensis)is one of the most important palms.However,the genome sequences of palms that are currently available are still limited and fragmented.Here,we report a high-quality chromosome-level reference genome of an oil palm,Dura,assembled by integrating long reads with～150x genome coverage.The assembled genome was 1.7 Gb in size,covering 94.5％of the estimated genome,of which 91.6％was assigned into 16 pseudochromosomes and 73.7％was repetitive sequences.Relying on the conserved synteny with oil palm,the existing draft genome sequences of both date palm and coconut were further assem-bled into chromosomal level.Transposon burst,particularly long terminal repeat retrotransposons,following the last whole-genome duplication,likely explains the genome size variation across palms.Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors.Recent duplications of highly tandemly repeated pathogenesis-related pro-teins from the same tandem arrays play an important role in defense responses to Ganoderma.Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses,suggesting adaptation to stresses in the new habitat.The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.
      原文链接:
    • 万方数据
    • 维普

    Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species,Cyclocarya paliurus

    Yinquan QuXulan ShangZiyan ZengYanhao Yu...
    455-469页
    查看更多>>摘要：Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently.Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B.Here,we presented three C.paliurus gen-omes from two diploids with different flower morphs and one haplotype-resolved tetraploid assem-bly.Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids.Resequencing analysis of 45 C.paliurus individuals uncovered two bottlenecks,consistent with the known events of environ-mental changes,and many selectively swept genes involved in critical biological functions,including plant defense and secondary metabolite biosynthesis.We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes,in particular gibberellin-related genes,associated with the heterodichogamy in C.paliurus species.Our study sheds light on evolutionary history of C.paliurus and provides genomic resources to study the medicinal herbs.
      原文链接:
    • 万方数据
    • 维普

    Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution

    Ruobing HanLei HanXunwu ZhaoQianghui Wang...
    470-482页
    查看更多>>摘要：Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed.To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae,we report,for the first time,a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies,which was anchored to 32 homologous groups with a pair of sex chromosomes(XY).Several expanded genes(RET,PPP2R1A,PPP2R1B,YWHAB,YWHAZ,and RPS6)and posi-tively selected genes(eIF4E,Wnt8A,Wnt9B,BMP4,and TP53)were identified,which could con-tribute to rapid antler growth without carcinogenesis.A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in reg-ulating rapid antler growth and inhibiting oncogenesis.Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer(Cervus elaphus),and the olfactory sensation of sika deer might be more powerful than that of red deer.Obvious inversion regions containing olfactory receptor genes were also identified,which arose since the divergence.In conclusion,the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler,chromosome evo-lution,and multi-omics research of cervid animals.
      原文链接:
    • 万方数据
    • 维普

    The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation

    Guobin ChangXiaoya YuanQixin GuoHao Bai...
    483-500页
    查看更多>>摘要：The Chinese crested(CC)duck is a unique indigenous waterfowl breed,which has a crest cushion that affects its survival rate.Therefore,the CC duck is an ideal model to investigate the ge-netic compensation response to maintain genetic stability.In the present study,we first generated a chromosome-level genome of CC ducks.Comparative genomics revealed that genes related to tissue repair,immune function,and tumors were under strong positive selection,indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic sta-bility of CC ducks.We also assembled a Chinese spot-billed(Csp-b)duck genome,and detected the structural variations(SVs)in the genome assemblies of three ducks(i.e.,CC duck,Csp-b duck,and Peking duck).Functional analysis revealed that several SVs were related to the immune system of CC ducks,further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks.Moreover,we confirmed that the CC duck originated from the mallard ducks.Finally,we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation.Overall,the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
      原文链接:
    • 万方数据
    • 维普

    Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation

    Jingqi ZhouAke LiuFunan HeYunbin Zhang...
    501-514页
    查看更多>>摘要：The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River system.As a rare freshwater-dwelling cartilagi-nous fish in the Potamotrygonidae family in which no member has the genome sequencing informa-tion available,P.leopoldi provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton formation.In this study,we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds,with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size.Our analysis shows that P.leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago.Moreover,two gene families related to the immune system(immunoglobulin heavy con-stant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in P.leopoldi only.We also identified the Hox gene clusters in P.leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P.leopoldi.The RNA sequencing data from P.leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expres-sion spectrum when compared to mammals.Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both P.leopoldi and Callorhinchus milii)could partly explain the absence of hard bone in their endoskeleton.Overall,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of P.leopoldi,as well as the genome evolution in cartilaginous fishes.
      原文链接:
    • 万方数据
    • 维普

    Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities

    Sébastien LeblancMarie A.BrunetJean-Fran?ois JacquesAmina M.Lekehal...
    515-534页
    查看更多>>摘要：Recent proteogenomic approaches have led to the discovery that regions of the transcrip-tome previously annotated as non-coding regions[i.e.,untranslated regions(UTRs),open reading frames overlapping annotated coding sequences in a different reading frame,and non-coding RNAs]frequently encode proteins,termed alternative proteins(altProts).This suggests that previ-ously identified protein-protein interaction(PPI)networks are partially incomplete because altProts are not present in conventional protein databases.Here,we used the proteogenomic resource Open-Prot and a combined spectrum-and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset,thereby revealing the presence of 261 altProts in the network.We found 19 genes encoding both an annotated(reference)and an alternative protein interacting with each other.Of the 117 altProts encoded by pseudogenes,38 are direct interactors of reference proteins encoded by their respective parental genes.Finally,we experimentally validate several interactions involving altProts.These data improve the blueprints of the human PPI net-work and suggest functional roles for hundreds of altProts.
      原文链接:
    • 万方数据
    • 维普

    Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL

    David Earl HostalleroLixuan WeiLiewei WangJunmei Cairns...
    535-550页
    查看更多>>摘要：Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized medicine.Here,we developed a deep learning framework called TINDL,completely trained on preclinical cancer cell lines(CCLs),to predict the response of cancer patients to different treatments.TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the sta-tistical discrepancies between CCLs and patient tumors.Moreover,by making the deep learning black box interpretable,this model identifies a small set of genes whose expression levels are predic-tive of drug response in the trained model,enabling identification of biomarkers of drug response.Using data from two large databases of CCLs and cancer tumors,we showed that this model can distinguish between sensitive and resistant tumors for 10(out of 14)drugs,outperforming various other machine learning models.In addition,our small interfering RNA(siRNA)knockdown experiments on 10 genes identified by this model for one of the drugs(tamoxifen)confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells,and seven of these genes in T47D cells.Furthermore,genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling pathways.In summary,this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in cancer.The code can be accessed at https://github.com/ddhostallero/tindl.
      原文链接:
    • 万方数据
    • 维普

    Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons

    Liang WangXiaojie WangChunqi LiuWei Xu...
    551-572页
    查看更多>>摘要：The expression of linear DNA sequence is precisely regulated by the three-dimensional(3D)architecture of chromatin.Morphine-induced aberrant gene networks of neurons have been extensively investigated;however,how morphine impacts the 3D genomic architecture of neurons is still unknown.Here,we applied digestion-ligation-only high-throughput chromosome conforma-tion capture(DLO Hi-C)technology to investigate the effects of morphine on the 3D chromatin architecture of primate cortical neurons.After receiving continuous morphine administration for 90 days on rhesus monkeys,we discovered that morphine re-arranged chromosome territories,with a total of 391 segmented compartments being switched.Morphine altered over half of the detected topologically associated domains(TADs),most of which exhibited a variety of shifts,followed by separating and fusing types.Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops.Moreover,all identified differentially expressed genes from the RNA sequencing data were mapped to the specific TAD boundaries or differential loops,and were further validated for changed expression.Collectively,an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated with morphine effects.Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
      原文链接:
    • 万方数据
    • 维普

    Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes

    Yan ZhangJingwen ZhangWei ZhangMohan Wang...
    573-588页
    查看更多>>摘要：Studies on the lung cancer genome are indispensable for developing a cure for lung can-cer.Whole-genome resequencing,genome-wide association studies,and transcriptome sequencing have greatly improved our understanding of the cancer genome.However,dysregulation of long-range chromatin interactions in lung cancer remains poorly described.To better understand the three-dimensional(3D)genomic interaction features of the lung cancer genome,we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase Ⅱ(RNAPⅡ),CCCTC-binding factor(CTCF),enhancer of zeste homolog 2(EZH2),and histone 3 lysine 27 trimethylation(H3K27me3)using long-read chromatin interac-tion analysis by paired-end tag sequencing(ChIA-PET).Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes,either through loops or domains,and their dis-tributions along the genome were distinct from and complementary to those associated with RNAPⅡ.Cancer-related genes were highly enriched with chromatin interactions,and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes,such as additional repressive interactions on FOXO4 and promoter-promoter interactions between NF1 and RNF135.Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes,suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes.These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.
      原文链接:
    • 万方数据
    • 维普