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  1. Deep neural networks (DNN) are a particular case of artificial neural networks (ANN) composed by multiple hidden layers, and have recently gained attention in genome-enabled prediction of complex traits. Yet, ...

    Authors: Tiago L. Passafaro, Fernando B. Lopes, João R. R. Dórea, Mark Craven, Vivian Breen, Rachel J. Hawken and Guilherme J. M. Rosa

    Citation: BMC Genomics 2020 21:771

    Content type: Research article

    Published on:

  2. Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this det...

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

    Citation: BMC Genomics 2020 21:770

    Content type: Research article

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  3. Birth weight is determined by the interplay between infant genetics and the intrauterine environment and is associated with several health outcomes in later life. Many studies have reported an association betw...

    Authors: Pontus Henriksson, Antonio Lentini, Signe Altmäe, David Brodin, Patrick Müller, Elisabet Forsum, Colm E. Nestor and Marie Löf

    Citation: BMC Genomics 2020 21:769

    Content type: Research article

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  4. Recent sequencing projects on early-diverging metazoans such as cnidarians, have unveiled a rich innate immunity gene repertoire; however, little is known about immunity gene regulation in the host’s early res...

    Authors: François Seneca, David Davtian, Laurent Boyer and Dorota Czerucka

    Citation: BMC Genomics 2020 21:768

    Content type: Research article

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  5. Bacillus subtilis strain NCD-2 is an excellent biocontrol agent against plant soil-borne diseases and shows broad-spectrum antifungal activities. This study aimed to explore some secondary metabolite biosynthetic...

    Authors: Zhenhe Su, Xiuye Chen, Xiaomeng Liu, Qinggang Guo, Shezeng Li, Xiuyun Lu, Xiaoyun Zhang, Peipei Wang, Lihong Dong, Weisong Zhao and Ping Ma

    Citation: BMC Genomics 2020 21:767

    Content type: Research article

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  6. Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 i...

    Authors: Daniela Kajihara, Chung-Chau Hon, Aimi Naim Abdullah, João Wosniak Jr, Ana Iochabel S. Moretti, Joice F. Poloni, Diego Bonatto, Kosuke Hashimoto, Piero Carninci and Francisco R. M. Laurindo

    Citation: BMC Genomics 2020 21:766

    Content type: Research article

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  7. Cytoplasmic male sterility (CMS) is very important in hybrid breeding. The restorer-of-fertility (Rf) nuclear genes rescue the sterile phenotype. Most of the Rf genes encode pentatricopeptide repeat (PPR) protein...

    Authors: Luyun Ning, Hao Wang, Dianrong Li, Yonghong Li, Kang Chen, Hongbo Chao, Huaixin Li, Jianjie He and Maoteng Li

    Citation: BMC Genomics 2020 21:765

    Content type: Research article

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  8. Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management thr...

    Authors: John T. Dobbs, Mee-Sook Kim, Nicklos S. Dudley, Ned B. Klopfenstein, Aileen Yeh, Robert D. Hauff, Tyler C. Jones, R. Kasten Dumroese, Philip G. Cannon and Jane E. Stewart

    Citation: BMC Genomics 2020 21:764

    Content type: Research article

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  9. A pregnant gilt infected with porcine reproductive and respiratory syndrome virus (PRRSV) can transmit the virus to her fetuses across the maternal-fetal-interface resulting in varying disease outcomes. Howeve...

    Authors: Angelica Van Goor, Alex Pasternak, Kristen Walker, Linjun Hong, Carolina Malgarin, Daniel J. MacPhee, John C. S. Harding and Joan K. Lunney

    Citation: BMC Genomics 2020 21:763

    Content type: Research article

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  10. Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gol...

    Authors: Wesley J. Delage, Julien Thevenon and Claire Lemaitre

    Citation: BMC Genomics 2020 21:762

    Content type: Research article

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  11. The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, u...

    Authors: Ilona Binenbaum, Hanifa Abu-Toamih Atamni, Georgios Fotakis, Georgia Kontogianni, Theodoros Koutsandreas, Eleftherios Pilalis, Richard Mott, Heinz Himmelbauer, Fuad A. Iraqi and Aristotelis A. Chatziioannou

    Citation: BMC Genomics 2020 21:761

    Content type: Research article

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  13. Patterns of gene expression can be dramatically different between males and females of the same species, in part due to genes on sex chromosomes. Here we test for sex differences in early transcriptomic respon...

    Authors: Ning Li, Ben A. Flanagan, MacKenzie Partridge, Elaine J. Huang and Suzanne Edmands

    Citation: BMC Genomics 2020 21:759

    Content type: Research article

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  14. Abiotic stress, including heat, is one of the major factors that affect alfalfa growth and forage yield. The small RNA, microRNA156 (miR156), regulates multiple traits in alfalfa during abiotic stress. The aim...

    Authors: Muhammad Arshad, Alpa Puri, Aaron J. Simkovich, Justin Renaud, Margaret Y. Gruber, Frédéric Marsolais and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:758

    Content type: Research article

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  15. Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3...

    Authors: Jaire A. Ferreira Filho, Maria Augusta C. Horta, Clelton A. dos Santos, Deborah A. Almeida, Natália F. Murad, Juliano S. Mendes, Danilo A. Sforça, Claudio Benício C. Silva, Aline Crucello and Anete P. de Souza

    Citation: BMC Genomics 2020 21:757

    Content type: Research article

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  16. Recent advances in single-cell RNA sequencing have allowed researchers to explore transcriptional function at a cellular level. In particular, single-cell RNA sequencing reveals that there exist clusters of ce...

    Authors: Florian Klimm, Enrique M. Toledo, Thomas Monfeuga, Fang Zhang, Charlotte M. Deane and Gesine Reinert

    Citation: BMC Genomics 2020 21:756

    Content type: Research article

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  17. With 9730 protein-coding genes and a nearly complete gene knockout strain collection, Neurospora crassa is a major model organism for filamentous fungi. Despite this abundance of information, the phenotypes of th...

    Authors: Alexander J. Carrillo, Ilva E. Cabrera, Marko J. Spasojevic, Patrick Schacht, Jason E. Stajich and Katherine A. Borkovich

    Citation: BMC Genomics 2020 21:755

    Content type: Research article

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  18. Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematic...

    Authors: Siddharth Sethi, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Simon Greenaway, John Williams, Vsevolod J. Makeev, Steve D. M. Brown, Michelle M. Simon and Ann-Marie Mallon

    Citation: BMC Genomics 2020 21:754

    Content type: Research article

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  19. The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—...

    Authors: Jinghui Li, Siyuan Xing, Guiping Zhao, Maiqing Zheng, Xinting Yang, Jiahong Sun, Jie Wen and Ranran Liu

    Citation: BMC Genomics 2020 21:752

    Content type: Research article

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  20. The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein codi...

    Authors: Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald and David W. Burt

    Citation: BMC Genomics 2020 21:751

    Content type: Research article

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  22. Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which i...

    Authors: Huiyan Wang, Ning Wang and Yixin Huo

    Citation: BMC Genomics 2020 21:749

    Content type: Research article

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  24. Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMeth...

    Authors: Yunsung Lee, Kristine L. Haftorn, William R. P. Denault, Haakon E. Nustad, Christian M. Page, Robert Lyle, Sindre Lee-Ødegård, Gunn-Helen Moen, Rashmi B. Prasad, Leif C. Groop, Line Sletner, Christine Sommer, Maria C. Magnus, Håkon K. Gjessing, Jennifer R. Harris, Per Magnus…

    Citation: BMC Genomics 2020 21:747

    Content type: Methodology article

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  25. In diploid cells, it is important to construct maternal and paternal Hi-C contact maps respectively since the two homologous chromosomes can differ in chromatin three-dimensional (3D) organization. Though prev...

    Authors: Han Luo, Xinxin Li, Haitao Fu and Cheng Peng

    Citation: BMC Genomics 2020 21:746

    Content type: Software

    Published on:

  26. Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene ...

    Authors: Qian Wang, Xiancai Hao, Kaiqiang Liu, Bo Feng, Shuo Li, Zhihua Zhang, Lili Tang, Shahid Mahboob and Changwei Shao

    Citation: BMC Genomics 2020 21:745

    Content type: Research article

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  27. Early diagnosis is crucial for effective medical management of cancer patients. Tissue biopsy has been widely used for cancer diagnosis, but its invasive nature limits its application, especially when repeated...

    Authors: Chitrita Goswami, Smriti Chawla, Deepshi Thakral, Himanshu Pant, Pramod Verma, Prabhat Singh Malik, Jayadeva, Ritu Gupta, Gaurav Ahuja and Debarka Sengupta

    Citation: BMC Genomics 2020 21:744

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:877

  28. Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been ver...

    Authors: Bai-Ling Chen, Wuttichai Mhuantong, Shih-Hsin Ho, Jo-Shu Chang, Xin-Qing Zhao and Feng-Wu Bai

    Citation: BMC Genomics 2020 21:743

    Content type: Research article

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  29. The production of foie gras involves different metabolic pathways in the liver of overfed ducks such as lipid synthesis and carbohydrates catabolism, but the establishment of these pathways has not yet been de...

    Authors: William Massimino, Stéphane Davail, Aurélie Secula, Charlotte Andrieux, Marie-Dominique Bernadet, Tracy Pioche, Karine Ricaud, Karine Gontier, Mireille Morisson, Anne Collin, Stéphane Panserat and Marianne Houssier

    Citation: BMC Genomics 2020 21:742

    Content type: Research article

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  30. Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental pro...

    Authors: Wenrui Li, Chuangfeng Liu, Jingling Liu, Zhenqing Bai and Zongsuo Liang

    Citation: BMC Genomics 2020 21:727

    Content type: Research article

    Published on:

  31. Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare ...

    Authors: Julie E. Hernández-Salmerón and Gabriel Moreno-Hagelsieb

    Citation: BMC Genomics 2020 21:741

    Content type: Methodology article

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  32. Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; ...

    Authors: Rui Gao, Chun-Lin Li, Xiao-Ling Tong, Min-Jin Han, Kun-Peng Lu, Shu-Bo Liang, Hai Hu, Yue Luan, Bi-Li Zhang, Yan-Yu Liu and Fang-Yin Dai

    Citation: BMC Genomics 2020 21:740

    Content type: Research article

    Published on:

  33. Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits,...

    Authors: Liang Wang, Brima Conteh, Linzhi Fang, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:739

    Content type: Research article

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  34. The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecul...

    Authors: Paulo Vieira, Jonathan Shao, Paramasivan Vijayapalani, Thomas R. Maier, Clement Pellegrin, Sebastian Eves-van den Akker, Thomas J. Baum and Lev G. Nemchinov

    Citation: BMC Genomics 2020 21:738

    Content type: Research article

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  35. Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from euryt...

    Authors: Lili Liu, Rong Zhang, Xiaowen Wang, Hua Zhu and Zhaohui Tian

    Citation: BMC Genomics 2020 21:737

    Content type: Research article

    Published on:

  36. TIFY is a plant-specific protein family with a diversity of functions in plant development and responses to stress and hormones, which contains JASMONATE ZIM-domain (JAZ), TIFY, PPD and ZML subfamilies. Despit...

    Authors: Xin He, Yu Kang, Wenqian Li, Wei Liu, Pan Xie, Li Liao, Luyao Huang, Min Yao, Lunwen Qian, Zhongsong Liu, Chunyun Guan, Mei Guan and Wei Hua

    Citation: BMC Genomics 2020 21:736

    Content type: Research article

    Published on:

  37. Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory ...

    Authors: Mohammad Aslam, Bello Hassan Jakada, Beenish Fakher, Joseph G. Greaves, Xiaoping Niu, Zhenxia Su, Yan Cheng, Shijiang Cao, Xiaomei Wang and Yuan Qin

    Citation: BMC Genomics 2020 21:735

    Content type: Research article

    Published on:

  38. Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transc...

    Authors: Zhaoxi Zhou, Hongmao Gao, Jianhong Ming, Zheli Ding, Xing’e Lin and Rulin Zhan

    Citation: BMC Genomics 2020 21:734

    Content type: Research article

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  39. Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has inc...

    Authors: Lisa Joos, Stien Beirinckx, Annelies Haegeman, Jane Debode, Bart Vandecasteele, Steve Baeyen, Sofie Goormachtig, Lieven Clement and Caroline De Tender

    Citation: BMC Genomics 2020 21:733

    Content type: Research article

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  40. Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mecha...

    Authors: Yi-Ling Chiu, Shinya Shikina, Yuki Yoshioka, Chuya Shinzato and Ching-Fong Chang

    Citation: BMC Genomics 2020 21:732

    Content type: Research article

    Published on:

  41. Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiologi...

    Authors: Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Cidan Yangji, Xiaoying Chen, Hui Jiang, Jincheng Zhong and Qiumei Ji

    Citation: BMC Genomics 2020 21:731

    Content type: Research article

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  42. Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in Cali...

    Authors: Peter Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish and Lynn Epstein

    Citation: BMC Genomics 2020 21:730

    Content type: Research article

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  44. The ray floret shapes referred to as petal types on the chrysanthemum (Chrysanthemum × morifolium Ramat.) capitulum is extremely abundant, which is one of the most important ornamental traits of chrysanthemum. Ho...

    Authors: Ya Pu, He Huang, Xiaohui Wen, Chenfei Lu, Bohan Zhang, Xueqi Gu, Shuai Qi, Guangxun Fan, Wenkui Wang and Silan Dai

    Citation: BMC Genomics 2020 21:728

    Content type: Research article

    Published on:

  45. Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries an...

    Authors: Zhe Qu, Wenyan Nong, Yifei Yu, Tobias Baril, Ho Yin Yip, Alexander Hayward and Jerome H. L. Hui

    Citation: BMC Genomics 2020 21:726

    Content type: Research article

    Published on:

  46. Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and ...

    Authors: Wenkai Du, Lihua Ning, Yongshun Liu, Shixi Zhang, Yuming Yang, Qing Wang, Shengqian Chao, Hui Yang, Fang Huang, Hao Cheng and Deyue Yu

    Citation: BMC Genomics 2020 21:725

    Content type: Research article

    Published on:

  47. Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic chan...

    Authors: Shelly A. Trigg, Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman and Steven B. Roberts

    Citation: BMC Genomics 2020 21:723

    Content type: Research article

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  48. The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The A...

    Authors: Nadeem Khan, Frank M. You, Raju Datla, Sridhar Ravichandran, Bosen Jia and Sylvie Cloutier

    Citation: BMC Genomics 2020 21:722

    Content type: Research article

    Published on:

  49. We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 mod...

    Authors: Biruk A. Feyissa, Justin Renaud, Vida Nasrollahi, Susanne E. Kohalmi and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:721

    Content type: Research article

    Published on:

  50. Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondria...

    Authors: Jigme Dorji, Christy J. Vander Jagt, Josie B. Garner, Leah C. Marett, Brett A. Mason, Coralie M. Reich, Ruidong Xiang, Emily L. Clark, Benjamin G. Cocks, Amanda J. Chamberlain, Iona M. MacLeod and Hans D. Daetwyler

    Citation: BMC Genomics 2020 21:720

    Content type: Research article

    Published on:

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