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  1. Content type: Research article

    Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequ...

    Authors: Qiuyun Wu, Junwei Wang, Shuxiang Mao, Haoran Xu, Qi Wu, Mantian Liang, Yiming Yuan, Mingyue Liu and Ke Huang

    Citation: BMC Genomics 2019 20:377

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  2. Content type: Research article

    Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, suc...

    Authors: Guojun Li, Menglu Hou, Yaxue Liu, Yue Pei, Minghui Ye, Yao Zhou, Chenxi Huang, Yaqi Zhao and Haoli Ma

    Citation: BMC Genomics 2019 20:375

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  3. Content type: Research article

    Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster ...

    Authors: Swati Sinha, Choy-Eng Nge, Chung Yan Leong, Veronica Ng, Sharon Crasta, Mohammad Alfatah, Falicia Goh, Kia-Ngee Low, Huibin Zhang, Prakash Arumugam, Alexander Lezhava, Swaine L. Chen, Yoganathan Kanagasundaram, Siew Bee Ng, Frank Eisenhaber and Birgit Eisenhaber

    Citation: BMC Genomics 2019 20:374

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  4. Content type: Research article

    Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. ...

    Authors: Guosong Wang, Long Jin, Yan Li, Qianzi Tang, Silu Hu, Hengyong Xu, Clare A. Gill, Mingzhou Li and Jiwen Wang

    Citation: BMC Genomics 2019 20:372

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  5. Content type: Research article

    Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a ra...

    Authors: Tong-jin Liu, You-jun Zhang, Niels Agerbirk, Hai-ping Wang, Xiao-chun Wei, Jiang-ping Song, Hong-ju He, Xue-zhi Zhao, Xiao-hui Zhang and Xi-xiang Li

    Citation: BMC Genomics 2019 20:371

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  6. Content type: Research article

    The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation ...

    Authors: Abhijeet Shah, Joseph I. Hoffman and Holger Schielzeth

    Citation: BMC Genomics 2019 20:370

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  7. Content type: Research article

    Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 f...

    Authors: Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang and Honghao Lv

    Citation: BMC Genomics 2019 20:369

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  8. Content type: Research article

    Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly ...

    Authors: Alltalents T. Murahwa, Fredrick Nindo, Harris Onywera, Tracy L. Meiring, Darren P. Martin and Anna-Lise Williamson

    Citation: BMC Genomics 2019 20:368

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  9. Content type: Research article

    Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids ...

    Authors: Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk and Zbigniew Zwierzykowski

    Citation: BMC Genomics 2019 20:367

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  10. Content type: Research article

    There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study de...

    Authors: Georgina Mansell, Tyler J. Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S. Schalkwyk, Jonathan Mill and Eilis Hannon

    Citation: BMC Genomics 2019 20:366

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  11. Content type: Software

    Data normalization and identification of significant differential expression represent crucial steps in RNA-Seq analysis. Many available tools rely on assumptions that are often not met by real data, including...

    Authors: Wentao Yang, Philip Rosenstiel and Hinrich Schulenburg

    Citation: BMC Genomics 2019 20:364

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  12. Content type: Research article

    The glyoxalase system usually comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII). This system converts cytotoxic methylglyoxal (MG) into non-toxic D-lactate in the presence of reduced glutath...

    Authors: Tiemei Li, Xin Cheng, Yuting Wang, Xiao Yin, Zhiqian Li, Ruiqi Liu, Guotian Liu, Yuejin Wang and Yan Xu

    Citation: BMC Genomics 2019 20:362

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  13. Content type: Research article

    Blood flow restoration is a definitive therapy for salvaging the myocardium following ischemic injury. Nevertheless, the sudden restoration of blood flow to the ischemic myocardium can induce ischemia-reperfus...

    Authors: Zanxin Wang, Junmin Wen, Chuzhi Zhou, Zhiwei Wang and Minxin Wei

    Citation: BMC Genomics 2019 20:361

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  14. Content type: Research article

    Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certa...

    Authors: Zhenpeng Li, Bo Pang, Duochun Wang, Jie Li, Jialiang Xu, Yujie Fang, Xin Lu and Biao Kan

    Citation: BMC Genomics 2019 20:360

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  15. Content type: Research article

    Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. ...

    Authors: Ida Djurdjevič, Tomasz Furmanek, Seita Miyazawa and Simona Sušnik Bajec

    Citation: BMC Genomics 2019 20:359

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  16. Content type: Research article

    In natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. He...

    Authors: Jochen Bathke, Anne Konzer, Bernhard Remes, Matthew McIntosh and Gabriele Klug

    Citation: BMC Genomics 2019 20:358

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  17. Content type: Research article

    Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are...

    Authors: Hugo Oliveira, Marta Sampaio, Luís D. R. Melo, Oscar Dias, Welkin H. Pope, Graham F. Hatfull and Joana Azeredo

    Citation: BMC Genomics 2019 20:357

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  18. Content type: Research article

    Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on sp...

    Authors: De-Long Guan, Rui-Rui Ding, Xiao-Yu Hu, Xing-Ran Yang, Sheng-Quan Xu, Wei Gu and Min Zhang

    Citation: BMC Genomics 2019 20:356

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  19. Content type: Research article

    Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties.

    Authors: Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Guili Yang, Hong Liu, Hui Wang, Zhiqiang Chen and Tao Guo

    Citation: BMC Genomics 2019 20:355

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  20. Content type: Research article

    Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evoluti...

    Authors: María Torres-Sánchez, David J. Gower, David Alvarez-Ponce, Christopher J. Creevey, Mark Wilkinson and Diego San Mauro

    Citation: BMC Genomics 2019 20:354

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  21. Content type: Research article

    Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples (Malus domestica). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal,...

    Authors: Changqing Ma, Bowen Liang, Bo Chang, Jiuying Yan, Li Liu, Ying Wang, Yazhou Yang and Zhengyang Zhao

    Citation: BMC Genomics 2019 20:353

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  22. Content type: Methodology article

    Gene-set analysis (GSA) has been commonly used to identify significantly altered pathways or functions from omics data. However, GSA often yields a long list of gene-sets, necessitating efficient post-processi...

    Authors: Sora Yoon, Jinhwan Kim, Seon-Kyu Kim, Bukyung Baik, Sang-Mun Chi, Seon-Young Kim and Dougu Nam

    Citation: BMC Genomics 2019 20:352

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  23. Content type: Research article

    Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mi...

    Authors: Anna I. Kolesnikova, Yuliya A. Putintseva, Evgeniy P. Simonov, Vladislav V. Biriukov, Natalya V. Oreshkova, Igor N. Pavlov, Vadim V. Sharov, Dmitry A. Kuzmin, James B. Anderson and Konstantin V. Krutovsky

    Citation: BMC Genomics 2019 20:351

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  24. Content type: Research article

    Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are neede...

    Authors: Qiaoqiao Zhu, Mukund Ramakrishnan, Jinhee Park and William J. Belden

    Citation: BMC Genomics 2019 20:350

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  25. Content type: Research article

    Palatoschisis or cleft palate is a known anomaly in pigs resulting in their death. However, little is known about its aetiology. A detailed description of the phenotype was derived from necropsy and by compute...

    Authors: Alexander Grahofer, Anna Letko, Irene Monika Häfliger, Vidhya Jagannathan, Alain Ducos, Olivia Richard, Vanessa Peter, Heiko Nathues and Cord Drögemüller

    Citation: BMC Genomics 2019 20:349

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  26. Content type: Research article

    Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridiz...

    Authors: Zengxiang Wu, Kaining Hu, Mengjiao Yan, Liping Song, Jing Wen, Chaozhi Ma, Jinxiong Shen, Tingdong Fu, Bin Yi and Jinxing Tu

    Citation: BMC Genomics 2019 20:348

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  27. Content type: Methodology article

    Single-cell RNA-sequencing (scRNA-seq) is fast becoming a powerful tool for profiling genome-scale transcriptomes of individual cells and capturing transcriptome-wide cell-to-cell variability. However, scRNA-s...

    Authors: Wenbin Ye, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yaru Su and Xiaohui Wu

    Citation: BMC Genomics 2019 20:347

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  28. Content type: Correction

    Following the publication of this article [1], the authors noted the following errors.

    Authors: Kai Bi, Tao Chen, Zhangchao He, Zhixiao Gao, Ying Zhao, Yanping Fu, Jiasen Cheng, Jiatao Xie and Daohong Jiang

    Citation: BMC Genomics 2019 20:346

    Published on:

    The original article was published in BMC Genomics 2018 19:881

  29. Content type: Research

    It was shown that the major part of human genome is transcribed and produces a large number of long noncoding RNAs (lncRNAs). Today there are many evidences that lncRNAs play important role in the regulation o...

    Authors: Daria O. Konina, Alexandra Yu. Filatova and Mikhail Yu. Skoblov

    Citation: BMC Genomics 2019 20(Suppl 3):298

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  30. Content type: Research

    The development of essential hypertension is associated with a wide range of mechanisms. The brain stem neurons are essential for the homeostatic regulation of arterial pressure as they control baroreflex and ...

    Authors: Larisa A. Fedoseeva, Leonid O. Klimov, Nikita I. Ershov, Vadim M. Efimov, Arcady L. Markel, Yuriy L. Orlov and Olga E. Redina

    Citation: BMC Genomics 2019 20(Suppl 3):297

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  31. Content type: Research

    Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by pr...

    Authors: Ruimin Wang, Yunlong Wang, Xueying Zhang, Yaliang Zhang, Xiaoyong Du, Yaping Fang and Guoliang Li

    Citation: BMC Genomics 2019 20(Suppl 3):296

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  32. Content type: Database

    Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great impo...

    Authors: Viktor N. Shamanskiy, Valeria N. Timonina, Konstantin Yu. Popadin and Konstantin V. Gunbin

    Citation: BMC Genomics 2019 20(Suppl 3):295

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

    The Correction to this article has been published in BMC Genomics 2019 20:556

  33. Content type: Research

    Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of ge...

    Authors: Andrey A. Yurchenko, Tatiana E. Deniskova, Nikolay S. Yudin, Arsen V. Dotsev, Timur N. Khamiruev, Marina I. Selionova, Sergey V. Egorov, Henry Reyer, Klaus Wimmers, Gottfried Brem, Natalia A. Zinovieva and Denis M. Larkin

    Citation: BMC Genomics 2019 20(Suppl 3):294

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  34. Content type: Research

    Structural homology modeling supported by bioinformatics analysis plays a key role in uncovering new molecular interactions within gene regulatory networks. Here, we have applied this powerful approach to anal...

    Authors: Nikita V. Ivanisenko, Jörn H. Buchbinder, Johannes Espe, Max Richter, Miriam Bollmann, Laura K. Hillert, Vladimir A. Ivanisenko and Inna N. Lavrik

    Citation: BMC Genomics 2019 20(Suppl 3):293

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    This article is part of a Supplement: Volume 20 Supplement 3

  35. Content type: Research

    Net blotch caused by Pyrenophra teres f. teres is a major foliar disease of barley. Infection can result in significant yield losses of susceptible cultivars of up to 40%. Of the two forms of net blotch (P. teres

    Authors: Irina V. Rozanova, Nina M. Lashina, Zakhar S. Mustafin, Sofia A. Gorobets, Vadim M. Efimov, Olga S. Afanasenko and Elena K. Khlestkina

    Citation: BMC Genomics 2019 20(Suppl 3):292

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    This article is part of a Supplement: Volume 20 Supplement 3

  36. Content type: Research article

    Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been forme...

    Authors: Dorcus Kholofelo Malomane, Henner Simianer, Annett Weigend, Christian Reimer, Armin Otto Schmitt and Steffen Weigend

    Citation: BMC Genomics 2019 20:345

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  37. Content type: Research article

    Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA se...

    Authors: H. Beiki, H. Liu, J. Huang, N. Manchanda, D. Nonneman, T. P. L. Smith, J. M. Reecy and C. K. Tuggle

    Citation: BMC Genomics 2019 20:344

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  38. Content type: Research article

    Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part ...

    Authors: Gui-Hua Li, Han-Cai Chen, Jia-Li Liu, Wen-Long Luo, Da-Sen Xie, Shao-Bo Luo, Ting-Quan Wu, Waheed Akram and Yu-Juan Zhong

    Citation: BMC Genomics 2019 20:343

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  39. Content type: Research article

    In our previous study, we identified four isoforms of the Bmovo gene, Bmovo-1, Bmovo-2, Bmovo-3 and Bmovo-4 from the silkworm ovary and verified that ovarian development was regulated by the BmOVO proteins. Resul...

    Authors: Min Zhu, Xiaolong Hu, Zi Liang, Mengsheng Jiang, Renyu Xue, Yongchang Gong, Xing Zhang, Guangli Cao and Chengliang Gong

    Citation: BMC Genomics 2019 20:342

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  40. Content type: Research article

    Elevated water temperature, as is expected through climate change, leads to masculinization in fish species with sexual plasticity, resulting in changes in population dynamics. These changes are one important ...

    Authors: Shahrbanou Hosseini, Ngoc-Thuy Ha, Henner Simianer, Clemens Falker-Gieske, Bertram Brenig, Andre Franke, Gabriele Hörstgen-Schwark, Jens Tetens, Sebastian Herzog and Ahmad Reza Sharifi

    Citation: BMC Genomics 2019 20:341

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  41. Content type: Research article

    Lysine crotonylation, as a novel evolutionarily conserved type of post-translational modifications, is ubiquitous and essential in cell biology. However, its functions in tea plants are largely unknown, and th...

    Authors: Jianhao Sun, Chen Qiu, Wenjun Qian, Yu Wang, Litao Sun, Yusheng Li and Zhaotang Ding

    Citation: BMC Genomics 2019 20:340

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  42. Content type: Research article

    Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hyd...

    Authors: Giorgio Gonnella, Nicole Adam and Mirjam Perner

    Citation: BMC Genomics 2019 20:339

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  43. Content type: Methodology article

    Bacteria carry a wide array of genes, some of which have multiple alleles. These different alleles are often responsible for distinct types of virulence and can determine the classification at the subspecies l...

    Authors: Lusine Khachatryan, Margriet E. M. Kraakman, Alexandra T. Bernards and Jeroen F. J. Laros

    Citation: BMC Genomics 2019 20:338

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  44. Content type: Research article

    Chinese cordyceps, also known as Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis), is of particular interest for its cryptic life cycle and economic and ecological importance. The lar...

    Authors: Xiao Li, Fen Wang, Qing Liu, Quanping Li, Zhengming Qian, Xiaoling Zhang, Kuan Li, Wenjia Li and Caihong Dong

    Citation: BMC Genomics 2019 20:337

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  45. Content type: Research article

    Triploid coho salmon are excellent models for studying gene dosage and the effects of increased cell volume on gene expression. Triploids have an additional haploid genome in each cell and have fewer but large...

    Authors: Kris A. Christensen, Dionne Sakhrani, Eric B. Rondeau, Jeffery Richards, Ben F. Koop and Robert H. Devlin

    Citation: BMC Genomics 2019 20:336

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  46. Content type: Research article

    The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod...

    Authors: Han Ming Gan, Frederic Grandjean, Tom L. Jenkins and Christopher Mervyn Austin

    Citation: BMC Genomics 2019 20:335

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  47. Content type: Research article

    Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitiv...

    Authors: Rute R. da Fonseca, Irene Ureña, Sandra Afonso, Ana Elisabete Pires, Emil Jørsboe, Lounès Chikhi and Catarina Ginja

    Citation: BMC Genomics 2019 20:334

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