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  1. Content type: Research article

    Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

    Authors: Haiping Du, Xiao Li, Lihua Ning, Rui Qin, Qing Du, Qing Wang, Haina Song, Fang Huang, Hui Wang and Deyue Yu

    Citation: BMC Genomics 2019 20:237

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  2. Content type: Research article

    The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adap...

    Authors: Isabelle Rosinski-Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart and Philippe Glaser

    Citation: BMC Genomics 2019 20:236

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  3. Content type: Research article

    Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic p...

    Authors: Pooja Yadav, K. B. Saxena, Anupama Hingane, C. V. Sameer Kumar, V. S. Kandalkar, Rajeev K. Varshney and Rachit K. Saxena

    Citation: BMC Genomics 2019 20:235

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  5. Content type: Research article

    Lactation and associated metabolic stresses during the post-partum period have been shown to impair fertility in dairy cows. The oviduct plays key roles in embryo development and the establishment of pregnancy...

    Authors: Yann Locatelli, Niamh Forde, Helmut Blum, Alexander Graf, Benoît Piégu, Pascal Mermillod, Eckhard Wolf, Patrick Lonergan and Marie Saint-Dizier

    Citation: BMC Genomics 2019 20:233

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  6. Content type: Research article

    Accumulation of protein aggregates are a major hallmark of progressive neurodegenerative disorders such as Parkinson’s disease and Alzheimer’s disease. Transgenic Caenorhabditis elegans nematodes expressing the h...

    Authors: Yiru A. Wang, Basten L. Snoek, Mark G. Sterken, Joost A. G. Riksen, Jana J. Stastna, Jan E. Kammenga and Simon C. Harvey

    Citation: BMC Genomics 2019 20:232

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  7. Content type: Methodology article

    We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome s...

    Authors: Tengguo Li, Elizabeth R. Unger and Mangalathu S. Rajeevan

    Citation: BMC Genomics 2019 20:231

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  8. Content type: Research article

    Flowering time and maturity are among the most important adaptive traits in soybean (Glycine max (L.) Merill). Flowering Locus T (FT) family genes function as key flowering integrators, with flowering-promoting m...

    Authors: Bingjun Jiang, Shouwei Zhang, Wenwen Song, Mohammad Abdul Awal Khan, Shi Sun, Chengsheng Zhang, Tingting Wu, Cunxiang Wu and Tianfu Han

    Citation: BMC Genomics 2019 20:230

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  10. Content type: Methodology article

    Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield...

    Authors: Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Frank Speleman and Kaat Durinck

    Citation: BMC Genomics 2019 20:228

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  11. Content type: Research article

    Abiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance ag...

    Authors: Deepika Verma, Neha Lakhanpal and Kashmir Singh

    Citation: BMC Genomics 2019 20:227

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  12. 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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  13. Content type: Methodology article

    Large-scale genetic screening using CRISPR-Cas9 technology has emerged as a powerful approach to uncover and validate gene functions. The ability to control the timing of genetic perturbation during CRISPR scr...

    Authors: Ning Sun, Sakina Petiwala, Rui Wang, Charles Lu, Mufeng Hu, Sujana Ghosh, Yan Hao, Christopher P. Miller and Namjin Chung

    Citation: BMC Genomics 2019 20:225

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  14. 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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  15. Content type: Research article

    Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is avai...

    Authors: S. M. Shivaraj, Rupesh Deshmukh, Humira Sonah and Richard R. Bélanger

    Citation: BMC Genomics 2019 20:222

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  16. Content type: Research article

    The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of ...

    Authors: Miriam Khider, Erik Hjerde, Hilde Hansen and Nils Peder Willassen

    Citation: BMC Genomics 2019 20:220

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  17. Content type: Research article

    Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination be...

    Authors: Isabela Tiemy Pereira, Lucia Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya and Bruno Dallagiovanna

    Citation: BMC Genomics 2019 20:219

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  18. 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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  19. Content type: Database Article

    Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can ob...

    Authors: Tong Liu, Jacob Porter, Chenguang Zhao, Hao Zhu, Nan Wang, Zheng Sun, Yin-Yuan Mo and Zheng Wang

    Citation: BMC Genomics 2019 20:217

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  20. Content type: Research article

    Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or...

    Authors: Jongsuk Chung, Ki-Wook Lee, Chung Lee, Seung-Ho Shin, Sungkyu Kyung, Hyo-Jeong Jeon, Sook-Young Kim, Eunjung Cho, Chang Eun Yoo, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Citation: BMC Genomics 2019 20:216

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  21. Content type: Research article

    Massively-parallel-sequencing, coupled with sample multiplexing, has made genetic tests broadly affordable. However, intractable index mis-assignments (commonly exceeds 1%) were repeatedly reported on some wid...

    Authors: Qiaoling Li, Xia Zhao, Wenwei Zhang, Lin Wang, Jingjing Wang, Dongyang Xu, Zhiying Mei, Qiang Liu, Shiyi Du, Zhanqing Li, Xinming Liang, Xiaman Wang, Hanmin Wei, Pengjuan Liu, Jing Zou, Hanjie Shen…

    Citation: BMC Genomics 2019 20:215

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  22. Content type: Research article

    Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, a...

    Authors: Zehong Ding, Weiwei Tie, Lili Fu, Yan Yan, Guanghua Liu, Wei Yan, Yanan Li, Chunlai Wu, Jiaming Zhang and Wei Hu

    Citation: BMC Genomics 2019 20:214

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  23. Content type: Research article

    Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability ...

    Authors: Shan-Shan Zhou, Zhen Xing, Hui Liu, Xian-Ge Hu, Qiong Gao, Jie Xu, Si-Qian Jiao, Kai-Hua Jia, Yu Qing Jin, Wei Zhao, Ilga Porth, Yousry A. El-Kassaby and Jian-Feng Mao

    Citation: BMC Genomics 2019 20:213

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  24. 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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  25. Content type: Research article

    Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a bi...

    Authors: Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki and Monika Schmoll

    Citation: BMC Genomics 2019 20:211

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  26. Content type: Research article

    The SnRK2s (Plant specific protein kinase) are involved in various biological processes, such as plant defense and environmental challenges. In Arabidopsis, AtSnRK2s regulate the expression of some metal transpor...

    Authors: Ruijiao Wang, Chao Wang, Qin Yao, Xue Xiao, Xing Fan, Lina Sha, Jian Zeng, Houyang Kang, Haiqin Zhang, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2019 20:210

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  27. Content type: Methodology article

    Massively parallel reporter assays (MPRAs) have emerged as a popular means for understanding noncoding variation in a variety of conditions. While a large number of experiments have been described in the liter...

    Authors: Leslie Myint, Dimitrios G. Avramopoulos, Loyal A. Goff and Kasper D. Hansen

    Citation: BMC Genomics 2019 20:209

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  29. Content type: Research article

    Halomicronema hongdechloris was the first cyanobacterium to be identified that produces chlorophyll (Chl) f. It contains Chl a and uses phycobiliproteins as its major light-harvesting components under white light...

    Authors: Min Chen, Miguel A. Hernandez-Prieto, Patrick C. Loughlin, Yaqiong Li and Robert D. Willows

    Citation: BMC Genomics 2019 20:207

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  30. Content type: Research article

    Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the n...

    Authors: Sarah Naiyer, Devinder Kaur, Jamaluddin Ahamad, Shashi Shekhar Singh, Yatendra Pratap Singh, Vivek Thakur, Alok Bhattacharya and Sudha Bhattacharya

    Citation: BMC Genomics 2019 20:206

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  31. Content type: Research article

    Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of...

    Authors: Mingqi Zhou, Natasha J. Sng, Collin E. LeFrois, Anna-Lisa Paul and Robert J. Ferl

    Citation: BMC Genomics 2019 20:205

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  32. 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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  33. Content type: Research article

    Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species...

    Authors: Claudio A. Valero-Jiménez, Javier Veloso, Martijn Staats and Jan A. L. van Kan

    Citation: BMC Genomics 2019 20:203

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  34. Content type: Research article

    Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanyin...

    Authors: Benjamín Planells, Isabel Gómez-Redondo, Eva Pericuesta, Patrick Lonergan and Alfonso Gutiérrez-Adán

    Citation: BMC Genomics 2019 20:202

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  36. Content type: Research article

    Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aur...

    Authors: M. Carla Piazzon, Ivona Mladineo, Fernando Naya-Català, Ron P. Dirks, Susanne Jong-Raadsen, Anamarija Vrbatović, Jerko Hrabar, Jaume Pérez-Sánchez and Ariadna Sitjà-Bobadilla

    Citation: BMC Genomics 2019 20:200

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  37. Content type: Research article

    Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The ai...

    Authors: Philip M. M. Ruppert, Jong-Gil Park, Xu Xu, Kyu Yeon Hur, Ann-Hwee Lee and Sander Kersten

    Citation: BMC Genomics 2019 20:199

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  38. Content type: Research article

    Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushr...

    Authors: Yunjiao Lüli, Qing Cai, Zuo H. Chen, Hu Sun, Xue-Tai Zhu, Xuan Li, Zhu L. Yang and Hong Luo

    Citation: BMC Genomics 2019 20:198

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  40. Content type: Research article

    Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and e...

    Authors: Vijay K. Sharma, Suryatej Akavaram, Robert G. Schaut and Darrell O. Bayles

    Citation: BMC Genomics 2019 20:196

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  41. 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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  42. Content type: Research article

    Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome se...

    Authors: Mei Liu, Lingzhao Fang, Shuli Liu, Michael G. Pan, Eyal Seroussi, John B. Cole, Li Ma, Hong Chen and George E. Liu

    Citation: BMC Genomics 2019 20:181

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  43. 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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  44. 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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  45. Content type: Research article

    The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analyti...

    Authors: G. Gebreyesus, A. J. Buitenhuis, N. A. Poulsen, M. H. P. W. Visker, Q. Zhang, H. J. F. van Valenberg, D. Sun and H. Bovenhuis

    Citation: BMC Genomics 2019 20:178

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  47. Content type: Database Article

    Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with para...

    Authors: Benjamin N. Bimber, Melissa Y. Yan, Samuel M. Peterson and Betsy Ferguson

    Citation: BMC Genomics 2019 20:176

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  48. Content type: Research article

    The phyla Cnidaria, Placozoa, Ctenophora, and Porifera emerged before the split of proto- and deuterostome animals, about 600 million years ago. These early metazoans are interesting, because they can give us ...

    Authors: Sofie K. D. Nielsen, Thomas L. Koch, Frank Hauser, Anders Garm and Cornelis J. P. Grimmelikhuijzen

    Citation: BMC Genomics 2019 20:175

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  49. 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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  50. Content type: Research article

    Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe ...

    Authors: Michela Ruinelli, Jochen Blom, Theo H. M. Smits and Joël F. Pothier

    Citation: BMC Genomics 2019 20:172

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