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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 1 of 17

  1. Content type: Research article

    Despite the tremendous therapeutic advances that have stemmed from somatic oncogenetics, survival of some cancers has not improved in 50 years. Osteosarcoma still has a 5-year survival rate of 66%. We propose ...

    Authors: Isain Zapata, Luis E. Moraes, Elise M. Fiala, Sara Zaldivar-Lopez, C. Guillermo Couto, Jennie L. Rowell and Carlos E. Alvarez

    Citation: BMC Genomics 2019 20:226

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  2. Content type: Research article

    Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, togeth...

    Authors: Charikleia Karageorgiou, Víctor Gámez-Visairas, Rosa Tarrío and Francisco Rodríguez-Trelles

    Citation: BMC Genomics 2019 20:223

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  3. Content type: Research article

    Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infec...

    Authors: Stephen R. Doyle, Christopher J. R. Illingworth, Roz Laing, David J. Bartley, Elizabeth Redman, Axel Martinelli, Nancy Holroyd, Alison A. Morrison, Andrew Rezansoff, Alan Tracey, Eileen Devaney, Matthew Berriman, Neil Sargison, James A. Cotton and John S. Gilleard

    Citation: BMC Genomics 2019 20:218

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  4. Content type: Research article

    Escherichia coli is an important pathogen that causes diarrhea in both humans and animals. To determine the relationships between putative virulence factors and pathotypes or host taxa, many molecular studies on ...

    Authors: Fang Tang, Juanfang Wang, Dezhi Li, Song Gao, Jianluan Ren, Liqing Ma, Fei Liu, Xiangkai Zhuge, Genqiang Yan, Yan Lu and Jianjun Dai

    Citation: BMC Genomics 2019 20:212

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  5. Content type: Research article

    In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as...

    Authors: Yoosook Lee, Hanno Schmidt, Travis C. Collier, William R. Conner, Mark J. Hanemaaijer, Montgomery Slatkin, John M. Marshall, Joanna C. Chiu, Chelsea T. Smartt, Gregory C. Lanzaro, F. Steve Mulligan and Anthony J. Cornel

    Citation: BMC Genomics 2019 20:204

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  6. Content type: Research article

    Although the importance of host plant chemistry in plant–insect interactions is widely recognized, our understanding about the genetic basis underlying the relationship between changes in midgut proteins and a...

    Authors: Zehai Hou and Cong Wei

    Citation: BMC Genomics 2019 20:182

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  7. Content type: Research article

    After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidizatio...

    Authors: Zhenyi Wang, Jinpeng Wang, Yuxin Pan, Tianyu Lei, Weina Ge, Li Wang, Lan Zhang, Yuxian Li, Kanglu Zhao, Tao Liu, Xiaoming Song, Jiaqi Zhang, Jigao Yu, Jingjing Hu and Xiyin Wang

    Citation: BMC Genomics 2019 20:180

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  8. Content type: Research article

    Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the isla...

    Authors: Pere Gelabert, Manuel Ferrando-Bernal, Toni de-Dios, Benedetta Mattorre, Elena Campoy, Amaya Gorostiza, Etienne Patin, Antonio González-Martín and Carles Lalueza-Fox

    Citation: BMC Genomics 2019 20:179

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  9. Content type: Research article

    The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure a...

    Authors: Gertrud Grilz-Seger, Thomas Druml, Markus Neuditschko, Max Dobretsberger, Michaela Horna and Gottfried Brem

    Citation: BMC Genomics 2019 20:174

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  10. Content type: Research article

    Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has be...

    Authors: Alongkorn Kurilung, Chantisa Keeratipusana, Prapat Suriyaphol, David J. Hampson and Nuvee Prapasarakul

    Citation: BMC Genomics 2019 20:168

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  11. Content type: Research article

    Saliva of mosquitoes contains anti-platelet, anti-clotting, vasodilatory, anti-complement and anti-inflammatory substances that help the blood feeding process. The salivary polypeptides are at a fast pace of e...

    Authors: Vera Margarete Scarpassa, Humbeto Julio Debat, Ronildo Baiatone Alencar, José Ferreira Saraiva, Eric Calvo, Bruno Arcà and José M. C. Ribeiro

    Citation: BMC Genomics 2019 20:166

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  12. Content type: Research article

    Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite t...

    Authors: Surabhi Srivastava, Akshay Kumar Avvaru, Divya Tej Sowpati and Rakesh K. Mishra

    Citation: BMC Genomics 2019 20:153

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  13. Content type: Research article

    Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of whe...

    Authors: Chengwei Wang, Yu Wang, Qi Pan, Shoukun Chen, Cuizhu Feng, Jiangbo Hai and Haifeng Li

    Citation: BMC Genomics 2019 20:142

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  14. Content type: Research article

    The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical ...

    Authors: Li Ma, Tad S. Sonstegard, John B. Cole, Curtis P. VanTassell, George R. Wiggans, Brian A. Crooker, Cheng Tan, Dzianis Prakapenka, George E. Liu and Yang Da

    Citation: BMC Genomics 2019 20:128

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  15. Content type: Research article

    Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossom...

    Authors: Dengwei Jue, Xuelian Sang, Liqin Liu, Bo Shu, Yicheng Wang, Chengming Liu, Yi Wang, Jianghui Xie and Shengyou Shi

    Citation: BMC Genomics 2019 20:126

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  16. Content type: Research article

    Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although th...

    Authors: Rick Masonbrink, Tom R. Maier, Usha Muppirala, Arun S. Seetharam, Etienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nathan T. Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves-van den Akker, Matthew Hudson, Andrew J. Severin and Thomas J. Baum

    Citation: BMC Genomics 2019 20:119

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  17. Content type: Research article

    Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary met...

    Authors: A. P. Vasav and V. T. Barvkar

    Citation: BMC Genomics 2019 20:116

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  18. Content type: Research article

    Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associate...

    Authors: A. A. Kampfraath, L. Klasson, S. Y. Anvar, R. H. A. M. Vossen, D. Roelofs, K. Kraaijeveld and J. Ellers

    Citation: BMC Genomics 2019 20:106

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  19. Content type: Research article

    Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus preda...

    Authors: Nathan D. McDonald, Abish Regmi, Daniel P. Morreale, Joseph D. Borowski and E. Fidelma Boyd

    Citation: BMC Genomics 2019 20:105

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  20. Content type: Research article

    Protein secretion is an essential process in all eukaryotes including organisms belonging to the phylum Apicomplexa, which includes many intracellular parasites. The apicomplexan parasites possess a specialize...

    Authors: K. M. Kaderi Kibria, Jannatul Ferdous, Rahila Sardar, Ashutosh Panda, Dinesh Gupta, Asif Mohmmed and Pawan Malhotra

    Citation: BMC Genomics 2019 20:98

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  21. Content type: Research article

    Toxoplasma gondii is an obligate intracellular parasite that infects humans and other warm-blooded animals. Previous quantitative proteomic analyses of infected host cells revealed that the expression of many hos...

    Authors: Zhaofeng Hou, Dandan Liu, Shijie Su, Lele Wang, Zhenxing Zhao, Yifei Ma, Qiaoqiao Li, Chuanli Jia, Jinjun Xu, Yonghua Zhou and Jianping Tao

    Citation: BMC Genomics 2019 20:97

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  22. Content type: Research article

    The SWEET proteins are a group of sugar transporters that play a role in sugar efflux during a range of biological processes, including stress responses. However, there has been no comprehensive analysis of the S...

    Authors: Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Xi Shan, Kan Bao, Li Yu, Hong Wang, Zhangjun Fei and Jianbin Li

    Citation: BMC Genomics 2019 20:93

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  23. Content type: Research article

    The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by you...

    Authors: Clemens Thölken, Markus Thamm, Christoph Erbacher and Marcus Lechner

    Citation: BMC Genomics 2019 20:88

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  24. Content type: Research article

    Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynth...

    Authors: Yongjun Wang, Xiuting Hua, Jingsheng Xu, Zhichang Chen, Tianqu Fan, Zhaohui Zeng, Hengbo Wang, Ai-Ling Hour, Qingyi Yu, Ray Ming and Jisen Zhang

    Citation: BMC Genomics 2019 20:83

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  25. Content type: Research article

    G-protein coupled receptors (GPCRs) are ancient, ubiquitous, constitute the largest family of transducing cell surface proteins, and are integral to cell communication via an array of ligands/neuropeptides. Mo...

    Authors: Nhut M. Tran, Donald L. Mykles, Abigail Elizur and Tomer Ventura

    Citation: BMC Genomics 2019 20:74

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  26. Content type: Research article

    The diversity of avian eggshell colour plays important biological roles in ensuring successful reproduction. Eggshell colour is also an important trait in poultry, but the mechanisms underlying it are poorly u...

    Authors: Ding-Ping Bai, Xin-Yu Lin, Yan Wu, Shi-Ye Zhou, Zhong-bin Huang, Yi-Fan Huang, Ang Li and Xiao-Hong Huang

    Citation: BMC Genomics 2019 20:66

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  27. Content type: Research article

    Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria...

    Authors: Dekang Zhu, Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Yu You, Xiaoyue Chen…

    Citation: BMC Genomics 2019 20:63

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  28. Content type: Research article

    Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a...

    Authors: Hui Wang, Zhixin Chai, Dan Hu, Qiumei Ji, Jinwei Xin, Chengfu Zhang and Jincheng Zhong

    Citation: BMC Genomics 2019 20:61

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  29. Content type: Research article

    Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adap...

    Authors: Rahul V. Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Goujie Zhang, Siu F. Lee, Ary A. Hoffmann and John G. Oakeshott

    Citation: BMC Genomics 2019 20:52

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  30. Content type: Research article

    Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichli...

    Authors: Athimed El Taher, Nicolás Lichilín, Walter Salzburger and Astrid Böhne

    Citation: BMC Genomics 2019 20:39

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  31. Content type: Review

    The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protei...

    Authors: Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo and John M. Archibald

    Citation: BMC Genomics 2019 20:38

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  32. Content type: Research article

    The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution an...

    Authors: Špela Alič, Jacques Pédron, Tanja Dreo and Frédérique Van Gijsegem

    Citation: BMC Genomics 2019 20:34

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  33. Content type: Research article

    Pathogens stimulate immune functions of macrophages. Macrophages are a key sentinel cell regulating the response to pathogenic ligands and orchestrating the direction of the immune response. Our study aimed at...

    Authors: Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka and Matthias Schweizer

    Citation: BMC Genomics 2019 20:15

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  34. Content type: Research article

    Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our know...

    Authors: Kai Kamm, Bernd Schierwater and Rob DeSalle

    Citation: BMC Genomics 2019 20:5

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  35. Content type: Research article

    Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and los...

    Authors: Zhong-Tao Yin, Feng Zhu, Fang-Bin Lin, Ting Jia, Zhen Wang, Dong-Ting Sun, Guang-Shen Li, Cheng-Lin Zhang, Jacqueline Smith, Ning Yang and Zhuo-Cheng Hou

    Citation: BMC Genomics 2019 20:4

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  36. Content type: Research article

    The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta

    Authors: Anastasiya E. Girnyk, Andrey A. Vergun, Seraphima K. Semyenova, Andrei S. Guliaev, Marine S. Arakelyan, Felix D. Danielyan, Irena A. Martirosyan, Robert W. Murphy and Alexey P. Ryskov

    Citation: BMC Genomics 2018 19:979

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  37. Content type: Research article

    Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim...

    Authors: Farzana Rahman, Mehedi Hassan, Abdulsamie Hanano, David A. Fitzpatrick, Charley G. P. McCarthy and Denis J. Murphy

    Citation: BMC Genomics 2018 19:976

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  38. Content type: Review

    Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DN...

    Authors: Mauno Vihinen

    Citation: BMC Genomics 2018 19:974

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  39. Content type: Research article

    The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, re...

    Authors: Olga O. Bochkareva, Elena V. Moroz, Iakov I. Davydov and Mikhail S. Gelfand

    Citation: BMC Genomics 2018 19:965

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  40. Content type: Research article

    Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of e...

    Authors: Tianjuan Su, Bo He, Kui Li and Aiping Liang

    Citation: BMC Genomics 2018 19:961

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  41. Content type: Research article

    Both human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considera...

    Authors: Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath and Matteo Pellegrini

    Citation: BMC Genomics 2018 19:956

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  42. Content type: Research article

    Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of comp...

    Authors: Sri Pratima Nandamuri, Matthew A. Conte and Karen L. Carleton

    Citation: BMC Genomics 2018 19:945

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  43. Content type: Software

    Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of ...

    Authors: Junwoo Bae, Kyeong Won Lee, Mohammad Nazrul Islam, Hyung-Soon Yim, Heejin Park and Mina Rho

    Citation: BMC Genomics 2018 19:944

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  44. Content type: Research article

    Unlike the chromosome constitution of most snakes (2n=36), the cobra karyotype shows a diploid chromosome number of 38 with a highly heterochromatic W chromosome and a large morphologically different chromosom...

    Authors: Worapong Singchat, Rebecca E. O’Connor, Panupong Tawichasri, Aorarat Suntronpong, Siwapech Sillapaprayoon, Sunutcha Suntrarachun, Narongrit Muangmai, Sudarath Baicharoen, Surin Peyachoknagul, Lawan Chanhome, Darren Griffin and Kornsorn Srikulnath

    Citation: BMC Genomics 2018 19:939

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  45. Content type: Research article

    The molecular mechanisms underlying stress-influenced immune function of chicken (Gallus Gallus) are not clear. The stress models can be established effectively by feeding chickens corticosterone (CORT) hormone. ...

    Authors: Yanhua Zhang, Yanting Zhou, Guirong Sun, Kui Li, Zhuanjian Li, Aru Su, Xiaojun Liu, Guoxi Li, Ruirui Jiang, Ruili Han, Yadong Tian, Xiangtao Kang and Fengbin Yan

    Citation: BMC Genomics 2018 19:918

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  46. Content type: Research article

    Comparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically sear...

    Authors: Rebecca Kirsch, Stefan E. Seemann, Walter L. Ruzzo, Stephen M. Cohen, Peter F. Stadler and Jan Gorodkin

    Citation: BMC Genomics 2018 19:899

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  47. Content type: Research article

    Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, a...

    Authors: Xiaoying Li, Yali Ma, Shuqing Liang, Yu Tian, Sanjun Yin, Sisi Xie and Hua Xie

    Citation: BMC Genomics 2018 19:889

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