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  1. Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major p...

    Authors: Santiago Diaz, Daniel Ariza-Suarez, Paulo Izquierdo, Juan David Lobaton, Juan Fernando de la Hoz, Fernando Acevedo, Jorge Duitama, Alberto F. Guerrero, Cesar Cajiao, Victor Mayor, Stephen E. Beebe and Bodo Raatz

    Citation: BMC Genomics 2020 21:799

    Content type: Research article

    Published on:

  2. Sperm miRNAs were reported to regulate spermatogenesis and early embryonic development in some mammals including bovine. The dairy cattle breeding industry now tends to collect semen from younger bulls under h...

    Authors: Chongyang Wu, Patrick Blondin, Christian Vigneault, Rémi Labrecque and Marc-André Sirard

    Citation: BMC Genomics 2020 21:798

    Content type: Research article

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  3. Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieti...

    Authors: Shaoshan Zhang, Qiong Liu, Chengcheng Lyu, Jinsong Chen, Renfeng Xiao, Jingtian Chen, Yunshu Yang, Huihui Zhang, Kai Hou and Wei Wu

    Citation: BMC Genomics 2020 21:794

    Content type: Research article

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  4. MYB superfamily is one of the most abundant families in plants, which plays important roles in plant growth, development, and productivity. However, to date, researches on MYBs in wheat (Triticum aestivum L.) are...

    Authors: Qiuhui Wei, Rong Chen, Xin Wei, Yuheng Liu, Shujuan Zhao, Xiaopu Yin and Tian Xie

    Citation: BMC Genomics 2020 21:792

    Content type: Research article

    Published on:

  5. RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short ...

    Authors: Beatrice T. Nganso, Noa Sela and Victoria Soroker

    Citation: BMC Genomics 2020 21:791

    Content type: Research article

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  6. Ophiocordyceps sinensis (Berk.) is a well-known entomopathogenic and medicinal fungus. It parasitizes and mummifies the underground ghost moth larvae to produce a fruiting body named Chinese cordyceps. Specific f...

    Authors: Miaomiao Li, Qian Meng, Huan Zhang, Ruihao Shu, Yanni Zhao, Peipei Wu, Xuan Li, Guiling Zhou, Qilian Qin and Jihong Zhang

    Citation: BMC Genomics 2020 21:789

    Content type: Research article

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  7. Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns i...

    Authors: Yuan Lu, Mikki Boswell, William Boswell, Raquel Ybanez Salinas, Markita Savage, Jose Reyes, Sean Walter, Rebecca Marks, Trevor Gonzalez, Geraldo Medrano, Wesley C. Warren, Manfred Schartl and Ronald B. Walter

    Citation: BMC Genomics 2020 21:787

    Content type: Research article

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  8. WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina ...

    Authors: Yanan Song, Hongli Cui, Ying Shi, Jinai Xue, Chunli Ji, Chunhui Zhang, Lixia Yuan and Runzhi Li

    Citation: BMC Genomics 2020 21:786

    Content type: Research article

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  9. Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochond...

    Authors: Sophie Dhorne-Pollet, Eric Barrey and Nicolas Pollet

    Citation: BMC Genomics 2020 21:785

    Content type: Methodology article

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  10. In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To rev...

    Authors: Da-Long Guo, Zhen-Guang Wang, Mao-Song Pei, Li-Li Guo and Yi-He Yu

    Citation: BMC Genomics 2020 21:784

    Content type: Research article

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  11. Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So ...

    Authors: Sèyi Fridaïus Ulrich Vanvanhossou, Carsten Scheper, Luc Hippolyte Dossa, Tong Yin, Kerstin Brügemann and Sven König

    Citation: BMC Genomics 2020 21:783

    Content type: Research article

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  12. Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain ...

    Authors: Di Wu, Anqi Liu, Xiaoyu Qu, Jiayi Liang and Min Song

    Citation: BMC Genomics 2020 21:782

    Content type: Research article

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  13. The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptatio...

    Authors: Guodong Chen, Jizhong Wang, Xin Qiao, Cong Jin, Weike Duan, Xiaochuan Sun and Juyou Wu

    Citation: BMC Genomics 2020 21:781

    Content type: Research article

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  14. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which d...

    Authors: Serafino M. A. Augustino, Qinglei Xu, Xueqin Liu, Siyuan Mi, Liangyu Shi, Yibing Liu, Hui Wen, Di Wang, Lei Liu, Qin Zhang and Ying Yu

    Citation: BMC Genomics 2020 21:780

    Content type: Research article

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  15. Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stre...

    Authors: Zahra Hajiahmadi, Amin Abedi, Hui Wei, Weibo Sun, Honghua Ruan, Qiang Zhuge and Ali Movahedi

    Citation: BMC Genomics 2020 21:778

    Content type: Research article

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  16. Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distingu...

    Authors: Oumar Diack, Ghislain Kanfany, Mame Codou Gueye, Ousmane Sy, Amadou Fofana, Hamidou Tall, Desalegn D. Serba, Leila Zekraoui, Cécile Berthouly-Salazar, Yves Vigouroux, Diaga Diouf and Ndjido Ardo Kane

    Citation: BMC Genomics 2020 21:777

    Content type: Research article

    Published on:

  17. Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, know...

    Authors: Hui Xia, Xiaosong Ma, Kai Xu, Lei Wang, Hongyan Liu, Liang Chen and Lijun Luo

    Citation: BMC Genomics 2020 21:776

    Content type: Research article

    Published on:

  18. Scylla paramamosain is one of the commercially crucial marine crustaceans belonging to the genus Scylla, which is commonly distributed along the coasts of China, Vietnam, and Japan. Genomic and transcriptomic dat...

    Authors: Na Li, Junming Zhou, Huan Wang, Changkao Mu, Ce Shi, Lei Liu and Chunlin Wang

    Citation: BMC Genomics 2020 21:775

    Content type: Research article

    Published on:

  19. Hibernation in an appropriate environment not only is important for the survival of hibernators in winter, but also is crucial for breeding in the following season for many hibernating species. However, the ge...

    Authors: Jian-Qing Lin, Jun Yu, Hua Jiang, Yi Zhang, Qiu-Hong Wan and Sheng-Guo Fang

    Citation: BMC Genomics 2020 21:774

    Content type: Research article

    Published on:

  20. Information on protein-protein interactions affected by mutations is very useful for understanding the biological effect of mutations and for developing treatments targeting the interactions. In this study, we...

    Authors: Jinchan Qu, Albert Steppi, Dongrui Zhong, Jie Hao, Jian Wang, Pei-Yau Lung, Tingting Zhao, Zhe He and Jinfeng Zhang

    Citation: BMC Genomics 2020 21:773

    Content type: Methodology article

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  21. Imputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference ...

    Authors: Isis da Costa Hermisdorff, Raphael Bermal Costa, Lucia Galvão de Albuquerque, Hubert Pausch and Naveen Kumar Kadri

    Citation: BMC Genomics 2020 21:772

    Content type: Research article

    Published on:

  22. 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:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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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  40. 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

    Published on:

  41. 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

    Published on:

  42. 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

    Published on:

  43. 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:

  44. 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

    Published on:

  45. 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:

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