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  2. Embryonic mortality is a major concern in the commercial swine industry and primarily occurs early in gestation, but also during mid-gestation (~ days 50–70). Previous reports demonstrated that the embryonic l...

    Authors: Kejun Wang, Kaijie Yang, Qiao Xu, Yufang Liu, Wenting Li, Ying Bai, Jve Wang, Cui Ding, Ximing Liu, Qiguo Tang, Yabiao Luo, Jie Zheng, Keliang Wu and Meiying Fang

    Citation: BMC Genomics 2019 20:991

    Content type: Research article

    Published on:

  3. Salinity has obvious effects on plant growth and crop productivity. The salinity-responsive mechanisms have been well-studied in differentiated organs (e.g., leaves, roots and stems), but not in unorganized ce...

    Authors: Yongxue Zhang, Yue Zhang, Juanjuan Yu, Heng Zhang, Liyue Wang, Sining Wang, Siyi Guo, Yuchen Miao, Sixue Chen, Ying Li and Shaojun Dai

    Citation: BMC Genomics 2019 20:990

    Content type: Research article

    Published on:

  4. Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variati...

    Authors: Priya Darshini Gurung, Atul Kumar Upadhyay, Pardeep Kumar Bhardwaj, Ramanathan Sowdhamini and Uma Ramakrishnan

    Citation: BMC Genomics 2019 20:989

    Content type: Research article

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  5. Vibrio spp. is the major infection-producing marine bacteria in commercially important bivalve Paphia undulata. The host resistance is the major determining factor for the development of pathogenesis. To explore ...

    Authors: Mingjia Yu, Lin Zheng, Xiaobo Wang, Minfu Wu, Ming Qi, Wandong Fu and Yang Zhang

    Citation: BMC Genomics 2019 20:988

    Content type: Research article

    Published on:

  6. As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, w...

    Authors: Minmin Li, Ying Liu, Yahan Tao, Chongjing Xu, Xin Li, Xiaoming Zhang, Yingpeng Han, Xue Yang, Jingzhe Sun, Wenbin Li, Dongmei Li, Xue Zhao and Lin Zhao

    Citation: BMC Genomics 2019 20:987

    Content type: Research article

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  7. Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one ...

    Authors: Ruibin Wang, Jingfei Ma, Qian Zhang, Chunlai Wu, Hongyan Zhao, Yanan Wu, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2019 20:986

    Content type: Research article

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  8. Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its ...

    Authors: Roshan Sharma Poudel, Jonathan Richards, Subidhya Shrestha, Shyam Solanki and Robert Brueggeman

    Citation: BMC Genomics 2019 20:985

    Content type: Research article

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  9. Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacterium that causes serious life threatening and nosocomial infections including pneumonia. PA has the ability to alter host genome to facilitate it...

    Authors: David L. Ebenezer, Panfeng Fu, Yashaswin Krishnan, Mark Maienschein-Cline, Hong Hu, Segun Jung, Ravi Madduri, Zarema Arbieva, Anantha Harijith and Viswanathan Natarajan

    Citation: BMC Genomics 2019 20:984

    Content type: Research article

    Published on:

  10. Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices base...

    Authors: Yanling Hu, Aihua Tan, Lei Yu, Chenyang Hou, Haofa Kuang, Qunying Wu, Jinghan Su, Qingniao Zhou, Yuanyuan Zhu, Chenqi Zhang, Wei Wei, Lianfeng Li, Weidong Li, Yuanjie Huang, Hongli Huang, Xing Xie…

    Citation: BMC Genomics 2019 20:983

    Content type: Research article

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  11. The plant homeodomain (PHD) finger is a Cys4HisCys3-type zinc finger which promotes protein-protein interactions and binds to the cis-acting elements in the promoter regions of target genes. In Medicago truncatul...

    Authors: Wenli Quan, Xun Liu, Lihua Wang, Mingzhu Yin, Li Yang and Zhulong Chan

    Citation: BMC Genomics 2019 20:982

    Content type: Research article

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  12. Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering...

    Authors: Adonis D’Mello, Christian P. Ahearn, Timothy F. Murphy and Hervé Tettelin

    Citation: BMC Genomics 2019 20:981

    Content type: Methodology article

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  14. The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in so...

    Authors: Jean F. Challacombe, Cedar N. Hesse, Lisa M. Bramer, Lee Ann McCue, Mary Lipton, Samuel Purvine, Carrie Nicora, La Verne Gallegos-Graves, Andrea Porras-Alfaro and Cheryl R. Kuske

    Citation: BMC Genomics 2019 20:976

    Content type: Research article

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  15. Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. A...

    Authors: Zhanru Shao, Pengyan Zhang, Chang Lu, Shaoxuan Li, Zhihang Chen, Xiuliang Wang and Delin Duan

    Citation: BMC Genomics 2019 20:975

    Content type: Research article

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  16. Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during ...

    Authors: Noémie Vimont, Mathieu Fouché, José Antonio Campoy, Meixuezi Tong, Mustapha Arkoun, Jean-Claude Yvin, Philip A. Wigge, Elisabeth Dirlewanger, Sandra Cortijo and Bénédicte Wenden

    Citation: BMC Genomics 2019 20:974

    Content type: Research article

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  17. Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fift...

    Authors: Amanda M. Vondras, Andrea Minio, Barbara Blanco-Ulate, Rosa Figueroa-Balderas, Michael A. Penn, Yongfeng Zhou, Danelle Seymour, Zirou Ye, Dingren Liang, Lucero K. Espinoza, Michael M. Anderson, M. Andrew Walker, Brandon Gaut and Dario Cantu

    Citation: BMC Genomics 2019 20:972

    Content type: Research article

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  18. The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential ro...

    Authors: Wei-wei Wang, Jing Wang, Hai-jun Zhang, Shu-geng Wu and Guang-hai Qi

    Citation: BMC Genomics 2019 20:970

    Content type: Research article

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  19. Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is ma...

    Authors: Shimin Fu, Jonathan Shao, Avijit Roy, Ronald H. Brlansky, Changyong Zhou and John S. Hartung

    Citation: BMC Genomics 2019 20:969

    Content type: Research article

    Published on:

  20. The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as...

    Authors: Paulo Rapazote-Flores, Micha Bayer, Linda Milne, Claus-Dieter Mayer, John Fuller, Wenbin Guo, Pete E. Hedley, Jenny Morris, Claire Halpin, Jason Kam, Sarah M. McKim, Monika Zwirek, M. Cristina Casao, Abdellah Barakate, Miriam Schreiber, Gordon Stephen…

    Citation: BMC Genomics 2019 20:968

    Content type: Research article

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  21. Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yell...

    Authors: Daiyan Li, Juwei Zhang, Haijiao Liu, Binwen Tan, Wei Zhu, Lili Xu, Yi Wang, Jian Zeng, Xing Fan, Lina Sha, Haiqin Zhang, Jian Ma, Guoyue Chen, Yonghong Zhou and Houyang Kang

    Citation: BMC Genomics 2019 20:963

    Content type: Research article

    Published on:

  22. Melanocytes are derived from neural crest stem cells in the embryonic stage. In mature melanocytes, a series of complex enzyme-catalyzed reactions leads to the production of melanins, which determine the hair ...

    Authors: Xuexian Liu, Bin Du, Pengqian Zhang, Junzhen Zhang, Zhiwei Zhu, Bo Liu and Ruiwen Fan

    Citation: BMC Genomics 2019 20:962

    Content type: Research article

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  23. During infection by intracellular pathogens, a highly complex interplay occurs between the infected cell trying to degrade the invader and the pathogen which actively manipulates the host cell to enable surviv...

    Authors: Jonas Kjellin, Maria Pränting, Frauke Bach, Roshan Vaid, Bart Edelbroek, Zhiru Li, Marc P. Hoeppner, Manfred Grabherr, Ralph R. Isberg, Monica Hagedorn and Fredrik Söderbom

    Citation: BMC Genomics 2019 20:961

    Content type: Research article

    Published on:

  24. Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorith...

    Authors: Javier Tamames, Marta Cobo-Simón and Fernando Puente-Sánchez

    Citation: BMC Genomics 2019 20:960

    Content type: Research article

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  25. Understanding the mechanisms by which organisms adapt to unfavourable conditions is a fundamental question in ecology and evolutionary biology. One such mechanism is diapause, a period of dormancy typically fo...

    Authors: Thomas J. Colgan, Sive Finlay, Mark J. F. Brown and James C. Carolan

    Citation: BMC Genomics 2019 20:959

    Content type: Research article

    Published on:

  27. After the extensive implementation of genomic selection (GS), the choice of the statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated fr...

    Authors: Hongding Gao, Per Madsen, Gert Pedersen Aamand, Jørn Rind Thomasen, Anders Christian Sørensen and Just Jensen

    Citation: BMC Genomics 2019 20:956

    Content type: Research article

    Published on:

  28. The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-g...

    Authors: Mao Qin, Shigang Wu, Alun Li, Fengli Zhao, Hu Feng, Lulu Ding and Jue Ruan

    Citation: BMC Genomics 2019 20:955

    Content type: Software

    Published on:

  29. Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less w...

    Authors: Yan-Xuan Zhang, Xia Chen, Jie-Ping Wang, Zhi-Qiang Zhang, Hui Wei, Hai-Yan Yu, Hong-Kun Zheng, Yong Chen, Li-Sheng Zhang, Jian-Zhen Lin, Li Sun, Dong-Yuan Liu, Juan Tang, Yan Lei, Xu-Ming Li and Min Liu

    Citation: BMC Genomics 2019 20:954

    Content type: Research article

    Published on:

  30. In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available ...

    Authors: Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Li Zhang, Hong Wu, Huan Liu, Ruiliang Zhu, Yu Jia, Bernard Goffinet and Yang Liu

    Citation: BMC Genomics 2019 20:953

    Content type: Research article

    Published on:

  31. Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most w...

    Authors: Vanessa Ferreira, José Tomás Matus, Olinda Pinto-Carnide, David Carrasco, Rosa Arroyo-García and Isaura Castro

    Citation: BMC Genomics 2019 20:952

    Content type: Research article

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  32. Mycobacterium smegmatis is a saprophytic bacterium frequently used as a genetic surrogate to study pathogenic Mycobacterium tuberculosis. The PrrAB two-component genetic regulatory system is essential in M. tuber...

    Authors: Jason D. Maarsingh, Shanshan Yang, Jin G. Park and Shelley E. Haydel

    Citation: BMC Genomics 2019 20:942

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2019 21:1

  34. Sperm epigenetics is an emerging area of study supported by observations reporting that abnormal sperm DNA methylation patterns are associated with infertility. Here, we explore cytosine-guanine dinucleotides ...

    Authors: Emanuele Capra, Barbara Lazzari, Federica Turri, Paola Cremonesi, Antônia Moemia Rodrigues Portela, Paolo Ajmone-Marsan, Alessandra Stella and Flavia Pizzi

    Citation: BMC Genomics 2019 20:940

    Content type: Research article

    Published on:

  35. Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists ab...

    Authors: Sara de las Heras-Saldana, Samuel A. Clark, Naomi Duijvesteijn, Cedric Gondro, Julius H. J. van der Werf and Yizhou Chen

    Citation: BMC Genomics 2019 20:939

    Content type: Research article

    Published on:

  36. Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the p...

    Authors: Yang Yang, Huiqiang Zhou, Liping Hou, Ke Xing and Hu Shu

    Citation: BMC Genomics 2019 20:938

    Content type: Research article

    Published on:

  38. Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still ...

    Authors: José Maria Gonzalez-Alba, Fernando Baquero, Rafael Cantón and Juan Carlos Galán

    Citation: BMC Genomics 2019 20:936

    Content type: Research article

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  39. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations...

    Authors: Shengrui Liu, Yanlin An, Wei Tong, Xiuju Qin, Lidia Samarina, Rui Guo, Xiaobo Xia and Chaoling Wei

    Citation: BMC Genomics 2019 20:935

    Content type: Research article

    Published on:

  40. MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aur...

    Authors: Shaoyang Ma, Chao Tong, Eveline M. Ibeagha-Awemu and Xin Zhao

    Citation: BMC Genomics 2019 20:934

    Content type: Research article

    Published on:

  41. Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population di...

    Authors: Qiong Wang, Yaxiong Jia, Yuan Wang, Zhihua Jiang, Xiang Zhou, Zebin Zhang, Changsheng Nie, Junying Li, Ning Yang and Lujiang Qu

    Citation: BMC Genomics 2019 20:933

    Content type: Research article

    Published on:

  42. Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages,...

    Authors: Xiaoyu Wang, Songling Zhu, Jian-Hua Zhao, Hong-Xia Bao, Huidi Liu, Tie-Min Ding, Gui-Rong Liu, Yong-Guo Li, Randal N. Johnston, Feng-Lin Cao, Le Tang and Shu-Lin Liu

    Citation: BMC Genomics 2019 20:930

    Content type: Research article

    Published on:

  43. Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide...

    Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker and Christopher M. Seabury

    Citation: BMC Genomics 2019 20:926

    Content type: Research article

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  44. Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB res...

    Authors: Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David J. Konkin, Ron E. Knox, Yuefeng Ruan and Pierre R. Fobert

    Citation: BMC Genomics 2019 20:925

    Content type: Research article

    Published on:

  45. Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a heal...

    Authors: Garima Raj, Mohammad Shadab, Sujata Deka, Manashi Das, Jilmil Baruah, Rupjyoti Bharali and Narayan C. Talukdar

    Citation: BMC Genomics 2019 20:924

    Content type: Research Article

    Published on:

  47. Prion diseases are zoonotic diseases with a broad infection spectrum among mammalian hosts and are caused by the misfolded prion protein (PrPSc) derived from the normal prion protein (PrPC), which encodes the pri...

    Authors: Yong-Chan Kim, Sae-Young Won and Byung-Hoon Jeong

    Citation: BMC Genomics 2019 20:922

    Content type: Research article

    Published on:

  48. Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis rema...

    Authors: Riëtte van Biljon, Roelof van Wyk, Heather J. Painter, Lindsey Orchard, Janette Reader, Jandeli Niemand, Manuel Llinás and Lyn-Marie Birkholtz

    Citation: BMC Genomics 2019 20:920

    Content type: Research article

    Published on:

  49. Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are...

    Authors: Kwanho Jeong, Alejandra Muñoz-Bodnar, Nathalia Arias Rojas, Lucie Poulin, Luis Miguel Rodriguez-R, Lionel Gagnevin, Christian Vernière, Olivier Pruvost and Ralf Koebnik

    Citation: BMC Genomics 2019 20:917

    Content type: Research article

    Published on:

  50. The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strai...

    Authors: Alex N. Salazar, Arthur R. Gorter de Vries, Marcel van den Broek, Nick Brouwers, Pilar de la Torre Cortès, Niels G. A. Kuijpers, Jean-Marc G. Daran and Thomas Abeel

    Citation: BMC Genomics 2019 20:916

    Content type: Research article

    Published on:

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