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Integrating Culture-based Antibiotic Resistance Profiles with whole-genome Sequencing Data for 11,087 Clinical Isolates

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Genomics, Proteomics & Bioinformatics 2019年第2期17卷 169-182页

作者： Valentina Galata Cédric C. Laczny Christina Backes Georg Hemmrich-Stanisak Susanne Schmolke Andre Franke Eckart Meese Mathias Herrmann Lutz von Müller Achim Plum Rolf Mü ller Cord Stahler Andreas E. Posch Andreas Keller Chair for Clinical Bioinformatics Saarland University 66123 Saarbrücken Germany Helmholtz Center for Infection Research and Pharmaceutical Biotechnology (HZI) Saarland University 66123 Saarbrücken Germany Institute of Clinical Molecular Biology Christian-Albrechts University of Kiel 24105 Kiel Germany Siemens Healthcare GmbH Strategy and Innovation 91052 Erlangen Germany Department of Human Genetics Saarland University 66421 Homburg Germany Institute of Medical Microbiology and Hygiene Saarland University 66421 Homburg Germany Ares Genetics GmbH 1030 Vienna Austria Curetis GmbH 71088 Holzgerlingen Germany Department of Pharmacy Pharmaceutical Biotechnology Saarland University 66123 Saarbrücken Germany Department of Microbial Natural Products Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Saarland University 66123 Saarbrücken Germany

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species,including conserved essential genes and known resis-tance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base,a resource available for academic research use free of charge at https://***.

关键词： Antibiotic resistance whole-genome sequencing Bacteria Pan-genome

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Molecular diagnosis of autosomal recessive cerebellar ataxia in the whole exome/genome sequencing era

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World Journal of Neurology 2013年第4期3卷 115-128页

作者： Christina Votsi Kyproula Christodoulou Neurogenetics Department The Cyprus Institute of Neurology and Genetics

Autosomal recessive cerebellar ataxias(ARCA) are a clinically and genetically heterogeneous group of rare neurodegenerative disorders characterized by autosomal recessive inheritance and an early age of onset. Progressive ataxia is usually the prominent symptom and is often associated with other neurological or additional features. ARCA classification still remains controversial even though different approaches have been proposed over the years. Furthermore, ARCA molecular diagnosis has been a challenge due to phenotypic overlap and increased genetic heterogeneity observed within this group of disorders. Friedreich's ataxia and ataxia telangiectasia have been reported as the most frequent and well-studied forms of ARCA. Significant progress in understanding the genetic etiologies of the ARCA has been achieved during the last 15 years. The methodological revolution that has been observed in genetics over the last few years has contributed significantly to the molecular diagnosis of rare diseases including the ARCAs. Development of high throughput technologies has resulted in the identification of new ARCA genes and novel mutations in known ARCA genes. Therefore,an improvement in the molecular diagnosis of ARCA is expected. Moreover, based on the fact that many patients still remain undiagnosed, additional forms of ataxia are expected to be identified. We hereby review the current knowledge on the ARCAs, focused on the genetic findings of the most common forms that were molecularly characterized before the whole exome/genome era, as well as the most recently described forms that have been elucidated with the use of these novel technologies. The significant contribution of wholeexome sequencing or whole-genome sequencing in the molecular diagnosis of ARCAs is discussed.

关键词： Autosomal recessive cerebellar ataxia whole-exome sequencing whole-genome sequencing Homozygosity mapping Next generation sequencing

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BRIF-Seq: Bisulfite-Converted Randomly Integrated Fragments Sequencing at the Single-Cell Level

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Molecular Plant 2019年第3期12卷 438-446页

作者： Xiang Li Lu Chen Qinghua Zhang Yonghao Sun Qing Li Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Single-cell bisulfite sequencing (scBS-seq) was developed to assess DNA methylation heterogeneity in human and mouse. However, the reads are under-represented in regions with high DNA methylation, because these regions are usually fragmented into long segments and are seldom sequenced on the lllumina plat. form. To reduce the read distribution bias and maximize the use of these long segments, we developed bisulfite-converted randomly integrated fragments sequencing (BRIF-seq), a method with high rates of read mapping and genome coverage. Single microspore of maize, which has a highly methylated and repetitive genome, was used to perform BRIF.seq. High coverage of the haploid genome was obtained to evaluate the methylation states of CG, CHG, and CHH (H = A, C, or T). Compared with scBS-seq, BRIF-seq produced reads that were distributed more evenly across the genome, including regions with high DNA methylation. Surprisingly, the methylation rates among the four microspores within one tetrad were similar, but differed significantly among tetrads, suggesting that non-simultaneous methylation reprogramming could occur among tetrads. Similar levels of heterogeneity, which often occur in lowcopy regions, were detected in different genetic backgrounds. These results suggest that BRIF-seq can be applied for single-cell methylome analysis of any species with diverse genetic backgrounds.

关键词： single-cell methylome whole-genome amplification reprogramming

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Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms

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Molecular Plant 2020年第1期13卷 59-71页

作者： Shengdan Wu Baocai Han Yuannian Jiao State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (～120 million years ago [Ma], ～66, and genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.

关键词： whole-genome duplication paleopolyploidy adaptive evolution phylogenomic Cretaceous-Paleocene boundary gene regulatory network

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The Chrysanthemum nankingense genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits

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Molecular Plant 2018年第12期11卷 1482-1491页

作者： Chi Song Yifei Liu Aiping Song Gangqiang Dong Hongbo Zhao Wei Sun Shyam Ramakrishnan Ying Wang Shuaibin Wang Tingzhao Li Yan Niu Jiafu Jiang Bin Dong Ye Xia Sumei Chen Zhigang Hu Fadi Chen Shilin Chen Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing 100700 China College of Pharmacy Hubei University of Chinese Medicine Wuhan 430065 China College of Horticulture Nanjing Agricultural University Key Laboratory of Landscape Agriculture Ministry of Agriculture Nanjing 210095 China Amway (China) Botanical R&D Center Wuxi 214115 China Department of Ornamental Horticulture School of Landscape Architecture Zhejiang Agriculture and Forestry University Hangzhou 311300 China Amway Corporation Buena Park CA 90622-5940 USA Wuhan Benagen Tech Solutions Company Limited Wuhan 430070 China Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden The Chinese Academy of Sciences Guangzhou 510650 China These authors contributed equally to this article

The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.)that diversified through reticulate evolution.Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication 0NGD)or polyploidization and locally repetitive genome expansion.However,the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification.Here,we used Oxford Nanopore long-read technologyto sequence the diploid Chrysanthemum nankingense genome,which represents one of the progenitor genomes of domesticated chrysanthemums.Our analysis revealed that the evolution of the C.nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recentWGD that distinguishes chrysanthemum from sunflower,which diverged from chrysanthemum approximately 38.8 million years ago.Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication.Collectively,our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants,and also to accelerate their breeding and improvement.

关键词： Chrysanthemum genome evolution whole-genome duplication nanopore sequencing flower evolution medicinal plant

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The genome of Cucurbita argyrosperma (Silver- Seed Gourd) Reveals Faster Rates of Protein- Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita

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Molecular Plant 2019年第4期12卷 506-520页

作者： Josue Barrera-Red on do Enrique Ibarra-Laclette Alejandra Vazquez-Lobo Yocelyn T. Gutierrez-Guerrero Guillermo Sanchez de la Vega Daniel Pinero Salvador Montes-Hernandez Rafael Lira-Saade Luis E. Eguiarte Departamento de Ecologia Evolutiva Instituto de Ecologia Universidad Nacional Aut6noma de Mexico Circuito Exterior s/n Anexo al Jardin Bot合nico 04510 Ciudad de Mexico Mexico Departamento de Estudios Moleculares Avanzados Instituto de Ecologia A.C. Carretera Antigua a Coatepec No. 351 Col. El Haya. C.P. Xalapa Veracruz 91070 Mexico Centro de Investigaciones en Biodiversidad y Conservacion Universidad Autdnoma del Estado de Morelos Av. Universidad 1001 Col. Chamilpa Cuernavaca Morelos 62209 Mexico Campo Experimental Bajio Instituto Nacional de In vestigaciones Forestales Agricolas y Pecuarias (INIFAP) Km 6.5 Carretera Celaya-San Miguel de Allen de Celaya Guanajuato 38110 Mexico UBIPRO Facultad de Estudios Superiores Iztacala Universidad Nacional Autdnoma de Mexico Av. de los Barrios #1 Col. Los Reyes Iztacala Tlanepantla Edo. de Mex 54090 Mexico

whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a wholegenome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, in eluding a newly assembled genome of Cucurbita argyrosperma, and compared the gene con tents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.

关键词： Cucurbita argyrosperma, comparative genomics molecular evolution neofunctionalization long noncoding RNA whole-genome duplication

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A Transcriptional Network Promotes Anthocyanin Biosynthesis in Tomato Flesh

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Molecular Plant 2020年第1期13卷 42-58页

作者： Chuanlong Sun Lei Deng Minmin Du Jiuhai Zhao Qian Chen Tingting Huang Hongling Jiang Chang-Bao Li Chuanyou Li State Key Laboratory of Plant Genomics National Centre for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China) Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTai'anShandong Province 271018China lnstitute of Vegetable Qingdao Academy of Agricultural SciencesQingdaoShandong Province 266100China

Dietary anthocyanins are important health-promoting antioxidants that make a major contribution to the quality of fruits. It is intriguing that most tomato cultivars do not produce anthocyanins in fruit. However, the purple tomato variety Indigo Rose, which has the dominant Aft locus combined with the recessive atv locus from wild tomato species, exhibits light-dependent anthocyanin accumulation in the fruit skin. Here, we report that Aft encodes a functional anthocyanin activator named SlAN2-like, while atv encodes a nonfunctional version of the anthocyanin repressor SlMYBATV. The expression of SlAN2-like is responsive to light, and the functional SlAN2-like can activate the expression of both anthocyanin biosynthetic genes and their regulatory genes, suggesting that SlAN2-like acts as a master regulator in the activation of anthocyanin biosynthesis. We further showed that cultivated tomatoes contain nonfunctional alleles of SlAN2-like and therefore fail to produce anthocyanins. Consistently, expression of a functional SlAN2-like gene driven by the fruit-specific promoter in a tomato cultivar led to the activation of the entire anthocyanin biosynthesis pathway and high-level accumulation of anthocyanins in both the peel and flesh. Taken together, our study exemplifies that efficient engineering of complex metabolic pathways could be achieved through tissue-specific expression of master transcriptional regulators.

关键词： whole-genome duplication paleopolyploidy adaptive evolution phylogenomic Cretaceous-Paleocene boundary gene regulatory network

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The Chromosome-Based Rubber Tree genome Provides New Insights into Spurge genome Evolution and Rubber Biosynthesis

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Molecular Plant 2020年第2期13卷 336-350页

作者： Jin Liu Cong Shi Cheng-Cheng Shi Wei Li Qun-Jie Zhang Yun Zhang Kui Li Hui-Fang Lu Chao Shi Si-Tao Zhu Zai-Yun Xiao Hong Nan Yao Yue Xun-Ge Zhu Yu Wu Xiao-Ning Hong Guang-Yi Fan Yan Tong Dan Zhang Chang-Li Mao Yun-Long Liu Shi-Jie Hao Wei-Qing Liu Mei-Qi Lv Hai-Bin Zhang Yuan Liu Ge-Ran Hu-tang Jin-Peng Wang Jia-Hao Wang Ying-Huai Sun Shu-Bang Ni Wen-Bin Chen Xing-Cai Zhang Yuan-Nian Jiao Evan E.Eichler Guo-Hua Li Xin Liu Li-Zhi Gao Yunnan Institute of Tropical Crops Jinghong 666100China Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern ChinaKunming Institute of BotanyChinese Academy of SciencesKunming 650204China University of Chinese Academy of Sciences Beijing 100049China BGI-Qingdao Qingdao 266555China lnstitution of Genomics and Bioinformatics South China Agricultural UniversityGuangzhou 510642China Asia-Pacific Tropical Forestry Germplasm Institution Southwest China Forestry UniversityKunming 650224China School of Life Sciences Nanjing UniversityNanjing 210023China Novogene Bioinformatics Institute Beijing 100083China BGI-Shenzhen Shenzhen 518083China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Howard Hughes Medical Institute University of WashingtonSeattleWA 98195USA

The rubber tree,Hevea brasiliensis,produces natural rubber that serves as an essential industrial raw material.Here,we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing(SMRT)and Hi-C technologies to anchor the～1.47-Gb genome assembly into 18 pseudochromosomes.The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution,since the common paleopolyploid event occurred before the split of Hevea and Manihot.We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years,leading to the massive expansion by～65.88%(～970 Mbp)of the whole rubber tree genome since the divergence from Manihot.We identify large-scale expansion of genes associated with whole rubber biosynthesis processes,such as basal metabolic processes,ethylene biosynthesis,and the activation of polysaccharide and glycoprotein lectin,which are important properties for latex production.A map of genomic variation between the cultivated and wild rubber trees was obtained,which contains～15.7 million high-quality single-nucleotide polymorphisms.We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree,some of which are involved in rubber biosynthesis.This genome assembly represents key resources for future rubber tree research and breeding,providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

关键词： rubber tree rubber biosynthesis chromosome evolution whole-genome duplication domestication

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Draft genome sequence of a less-known wild Vigna: Beach pea(V. marina cv. ANBp-14-03)

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The Crop Journal 2019年第5期7卷 660-666页

作者： Awnindra Kumar Singh A.Velmurugan Debjyoti Sen Gupta Jitendra Kumar Ravi Kesari Aravind Konda Narendra Pratap Singh Sibnarayan Dam Roy Utpal Biswas R.Rahul Kumar Sanjay Singh ICAR-Central Island Agricultural Research Institute Port Blair 744101Andaman&Nicobar IslandsIndia Division of Crop Improvement ICAR-Indian Institute of Pulses ResearchKanpur 208024Uttar PradeshIndia Department of Plant Breeding and Genetics Bhola Paswan Shastri Agricultural CollegePurneaBihar 854302India Division of Plant Biotechnology ICAR-Indian Institute of Pulses ResearchKanpur 208024Uttar PradeshIndia ICAR-National Research Centre for Biotechnology LBS CentrePusa CampusNew Delhi 110012India

Beach pea or beach cowpea(Vigna marina(Burm.)Merr.)belongs to the family Fabaceae.It is a close relative of cultivated Vigna species such as adzuki bean(V.angularis),cowpea(V.unguiculata),mung bean(V.radiata),and blackgram(V.mungo),and is distributed throughout the tropics.With its ability to tolerate salt stress,beach pea has great potential to contribute salt-tolerance genes for developing salt-tolerant cultivars in cultivated Vigna species.However,it is still underutilized in Vigna breeding programs.A draft genome sequence of beach pea was generated using a high-throughput next-generation sequencing platform,yielding 23.7 Gb of sequence from 79,929,868 filtered reads.A de novo genome assembly containing 68,731 scaffolds gave an N50 length of 10,272 bp and the assembled sequences totaled 365.6 Mb.A total of 35,448 SSRs,including 3574 compound SSRs,were identified and primer pairs for most of these SSRs were designed.genome analysis identified 50,670 genes with mean coding sequence length 1042 bp.Phylogenetic analysis revealed highest sequence similarity with V.angularis,followed by V.radiata.Comparison with the V.angularis genome revealed 16,699 SNPs and 2253 InDels and comparison with the V.radiata genome revealed 17,538 SNPs and 2300 InDels.To our knowledge this is the first draft genome sequence of beach pea derived from an accession(ANBp-14-03)adapted locally in the Andaman and Nicobar Islands of India.The draft genome sequence may facilitate the genetic enhancement in cultivated Vigna species.

关键词： Beach pea Vigna marina NextSeq 500 whole-genome sequencing Salinity tolerance

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BitmapAligner:Bit-Parallelism String Matching with MapReduce and Hadoop

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Computers, Materials & Continua 2021年第9期68卷 3931-3946页

作者： Mary Aksa Junaid Rashid Muhammad Wasif Nisar Toqeer Mahmood Hyuk-Yoon Kwon Amir Hussain Department of Computer Science COMSATS University IslamabadWah47040Pakistan Department of Computer Science AIR University IslamabadAerospace and Aviation Campus Kamra43570Pakistan Department of Computer Science National Textile UniversityFaisalabad37610Pakistan Department of Industrial Engineering and Research Center for Electrical and Information Technology Seoul National University of Science and TechnologyNowon-GuSeoul01811Korea Data Science and Cyber Analytics Research Group Edinburgh Napier UniversityEdinburghEH114DYUK

Advancements in next-generation sequencer(NGS)platforms have improved NGS sequence data production and reduced the cost involved,which has resulted in the production of a large amount of genome data.The downstream analysis of multiple associated sequences has become a bottleneck for the growing genomic data due to storage and space utilization issues in the domain of bioinformatics.The traditional string-matching algorithms are efficient for small sized data sequences and cannot process large amounts of data for downstream analysis.This study proposes a novel bit-parallelism algorithm called BitmapAligner to overcome the issues faced due to a large number of sequences and to improve the speed and quality of multiple sequence alignment(MSA).The input files(sequences)tested over BitmapAligner can be easily managed and organized using the Hadoop distributed file system.The proposed aligner converts the test file(the whole genome sequence)into binaries of an equal length of the sequence,line by line,before the sequence alignment processing.The Hadoop distributed file system splits the larger files into blocks,based on a defined block size,which is 128 MB by default.BitmapAligner can accurately process the sequence alignment using the bitmask approach on large-scale sequences after sorting the data.The experimental results indicate that BitmapAligner operates in real time,with a large number of sequences.Moreover,BitmapAligner achieves the exact start and end positions of the pattern sequence to test the MSA application in the whole genome query sequence.The MSA’s accuracy is verified by the bitmask indexing property of the bit-parallelism extended shifts(BXS)algorithm.The dynamic and exact approach of the BXS algorithm is implemented through the MapReduce function of Apache Hadoop.Conversely,the traditional seeds-and-extend approach faces the risk of errors while identifying the pattern sequences’positions.Moreover,the proposed model resolves the largescale data challenges that are covered through MapReduce in the Ha

关键词： Next-generation sequencing multiple sequence alignment MapReduce Hadoop whole-genome big data bit-parallelism

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