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  1. Processing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstac...

    Authors: Jayanthi Gangiredla, Hugh Rand, Daniel Benisatto, Justin Payne, Charles Strittmatter, Jimmy Sanders, William J. Wolfgang, Kevin Libuit, James B. Herrick, Melanie Prarat, Magaly Toro, Thomas Farrell and Errol Strain

    Citation: BMC Genomics 2021 22:114

    Content type: Software

    Published on:

  2. Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses ...

    Authors: Daniel Restrepo-Montoya, Phillip E. McClean and Juan M. Osorno

    Citation: BMC Genomics 2021 22:113

    Content type: Research article

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  3. In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived...

    Authors: Madoka Vera Krick, Erick Desmarais, Athanasios Samaras, Elise Guéret, Arkadios Dimitroglou, Michalis Pavlidis, Costas Tsigenopoulos and Bruno Guinand

    Citation: BMC Genomics 2021 22:111

    Content type: Research article

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  4. The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantit...

    Authors: Klavdija Pačnik, Mojca Ogrizović, Matthias Diepold, Tobias Eisenberg, Mia Žganjar, Gašper Žun, Beti Kužnik, Cene Gostinčar, Tomaž Curk, Uroš Petrovič and Klaus Natter

    Citation: BMC Genomics 2021 22:110

    Content type: Research article

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  5. Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very li...

    Authors: Wei Wang, Lei Wang, Ling Wang, Meilian Tan, Collins O. Ogutu, Ziyan Yin, Jian Zhou, Jiaomei Wang, Lijun Wang and Xingchu Yan

    Citation: BMC Genomics 2021 22:109

    Content type: Research article

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  6. In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist i...

    Authors: Maulana M. Naji, Yuri T. Utsunomiya, Johann Sölkner, Benjamin D. Rosen and Gábor Mészáros

    Citation: BMC Genomics 2021 22:108

    Content type: Research article

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  7. Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, wh...

    Authors: Shinji Sasaki, Youko Miki, Takayuki Ibi, Hiroyuki Wakaguri, Yuichi Yoshida, Yoshikazu Sugimoto and Yutaka Suzuki

    Citation: BMC Genomics 2021 22:107

    Content type: Research article

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  8. The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the Escherichia coli degradosome, PNPase is involved in maintaining proper RNA levels ...

    Authors: Daniel-Timon Spanka, Carina Maria Reuscher and Gabriele Klug

    Citation: BMC Genomics 2021 22:106

    Content type: Research article

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  9. Dissolved oxygen (DO) in the water is a vital abiotic factor in aquatic animal farming. A hypoxic environment affects the growth, metabolism, and immune system of fish. Glycolipid metabolism is a vital energy ...

    Authors: Jun-Lei Ma, Jun Qiang, Yi-Fan Tao, Jing-Wen Bao, Hao-Jun Zhu, Lian-Ge Li and Pao Xu

    Citation: BMC Genomics 2021 22:105

    Content type: Research article

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  10. Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the uni...

    Authors: Yiheng Wang, Sheng Wang, Yanlei Liu, Qingjun Yuan, Jiahui Sun and Lanping Guo

    Citation: BMC Genomics 2021 22:103

    Content type: Research article

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  11. Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the ...

    Authors: Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez and Edoardo Saccenti

    Citation: BMC Genomics 2021 22:102

    Content type: Research article

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  12. With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been...

    Authors: Jamal Momeni, Melanie Parejo, Rasmus O. Nielsen, Jorge Langa, Iratxe Montes, Laetitia Papoutsis, Leila Farajzadeh, Christian Bendixen, Eliza Căuia, Jean-Daniel Charrière, Mary F. Coffey, Cecilia Costa, Raffaele Dall’Olio, Pilar De la Rúa, M. Maja Drazic, Janja Filipi…

    Citation: BMC Genomics 2021 22:101

    Content type: Methodology article

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  13. Cataracts are defects of the lens that cause progressive visual impairment and ultimately blindness in many vertebrate species. Most cataracts are age-related, but up to one third have an underlying genetic ca...

    Authors: Chao Bai, Yuyan You, Xuefeng Liu, Maohua Xia, Wei Wang, Ting Jia, Tianchun Pu, Yan Lu, Chenglin Zhang, Xiaoguang Li, Yanqiang Yin, Liqin Wang, Jun Zhou and Lili Niu

    Citation: BMC Genomics 2021 22:100

    Content type: Research article

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  14. Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with h...

    Authors: Peipei Wang, Fanrui Meng, Bethany M. Moore and Shin-Han Shiu

    Citation: BMC Genomics 2021 22:99

    Content type: Research article

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  15. Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed ...

    Authors: Fuhui Han, Jing Li, Ranran Zhao, Lirong Liu, Lanlan Li, Qian Li, Jianning He and Nan Liu

    Citation: BMC Genomics 2021 22:98

    Content type: Research article

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  16. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Gurusamy Raman, Kyu Tae Park, Joo-Hwan Kim and SeonJoo Park

    Citation: BMC Genomics 2021 22:97

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:855

  17. Despite the increasing use of RNAseq for transcriptome analysis, microarrays remain a widely-used methodology for genomic studies. The latest generation of Affymetrix/Thermo-Fisher microarrays, the ClariomD/XT...

    Authors: Guy M. Harris, Shahroze Abbas and Michael F. Miles

    Citation: BMC Genomics 2021 22:96

    Content type: Software

    Published on:

  18. Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity a...

    Authors: Ligang Wang, Zhong-Yin Zhou, Tian Zhang, Longchao Zhang, Xinhua Hou, Hua Yan and Lixian Wang

    Citation: BMC Genomics 2021 22:95

    Content type: Research article

    Published on:

  19. Paeonia lactiflora ‘Hangshao’ is widely cultivated in China as a traditional Chinese medicine ‘Radix Paeoniae Alba’. Due to the abundant unsaturated fatty acids in its seed, it can also be regarded as a new oilse...

    Authors: Jia-Song Meng, Yu-Han Tang, Jing Sun, Da-Qiu Zhao, Ke-Liang Zhang and Jun Tao

    Citation: BMC Genomics 2021 22:94

    Content type: Research article

    Published on:

  20. The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miR...

    Authors: Lan Yu, Rongkai Guo, Yeqin Jiang, Xinghuo Ye, Zhihong Yang, Yijun Meng and Chaogang Shao

    Citation: BMC Genomics 2021 22:93

    Content type: Research article

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  21. One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality. Previously, we showed that a 50 K transcribed-SNP chip can be used to detect quantitati...

    Authors: Rafet Al-Tobasei, Ali Ali, Andre L. S. Garcia, Daniela Lourenco, Tim Leeds and Mohamed Salem

    Citation: BMC Genomics 2021 22:92

    Content type: Research article

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  22. The fungicide fludioxonil over-stimulates the fungal response to osmotic stress, leading to over-accumulation of glycerol and hyphal swelling and bursting. Fludioxonil-resistant fungal strains that are null-mu...

    Authors: Akeem O. Taiwo, Lincoln A. Harper and Mark C. Derbyshire

    Citation: BMC Genomics 2021 22:91

    Content type: Research article

    Published on:

  23. Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main trans...

    Authors: Wei Li, Ziwen Geng, Cuiping Zhang, Kuiling Wang and Xinqiang Jiang

    Citation: BMC Genomics 2021 22:90

    Content type: Research article

    Published on:

  24. Hair follicle density influences wool fibre production, which is one of the most important traits of the Wan Strain Angora rabbit. However, molecular mechanisms regulating hair follicle density have remained e...

    Authors: Haisheng Ding, Huiling Zhao, Xiaowei Zhao, Yunxia Qi, Xiaofei Wang and Dongwei Huang

    Citation: BMC Genomics 2021 22:89

    Content type: Research article

    Published on:

  25. Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real...

    Authors: Jianqing Chen, Jinyu Zhou, Yanhong Hong, Zekun Li, Xiangyu Cheng, Aiying Zheng, Yilin Zhang, Juanjuan Song, Guifeng Xie, Changmei Chen, Meng Yuan, Tengyun Wang and Qingxi Chen

    Citation: BMC Genomics 2021 22:88

    Content type: Research article

    Published on:

  26. More accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively err...

    Authors: Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis and Tariq M. Butt

    Citation: BMC Genomics 2021 22:87

    Content type: Research article

    Published on:

  27. The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total...

    Authors: Hua Zhong, Shuai Liu, Xiaoxi Meng, Tong Sun, Yujuan Deng, Weilong Kong, Zhaohua Peng and Yangsheng Li

    Citation: BMC Genomics 2021 22:86

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:206

  28. Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have ...

    Authors: Lingling Dou, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Haihong Shang, Hongbin Li and Guanghui Xiao

    Citation: BMC Genomics 2021 22:85

    Content type: Research article

    Published on:

  29. Co-localized combinations of histone modifications (“chromatin states”) have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points (“chromatin state...

    Authors: Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander and Uwe Ohler

    Citation: BMC Genomics 2021 22:84

    Content type: Methodology article

    Published on:

  30. Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifest...

    Authors: Xue Zhu, Jiyue Qin, Chongyang Tan and Kang Ning

    Citation: BMC Genomics 2021 22:83

    Content type: Research article

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  31. Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here...

    Authors: Pan Zhang, Tianqi Duo, Fengdan Wang, Xunzhong Zhang, Zouzhuan Yang and Guofu Hu

    Citation: BMC Genomics 2021 22:82

    Content type: Research article

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  32. The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic st...

    Authors: Mirosław Tyrka, Monika Mokrzycka, Beata Bakera, Dorota Tyrka, Magdalena Szeliga, Stefan Stojałowski, Przemysław Matysik, Michał Rokicki, Monika Rakoczy-Trojanowska and Paweł Krajewski

    Citation: BMC Genomics 2021 22:81

    Content type: Research article

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  33. Apoptosis is an important process for an organism’s innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key pr...

    Authors: Susanne Vogeler, Stefano Carboni, Xiaoxu Li and Alyssa Joyce

    Citation: BMC Genomics 2021 22:80

    Content type: Research article

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  34. Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberelli...

    Authors: Rongfa Chen, Yegeng Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yangrui Li, Lihang Qiu and Jianming Wu

    Citation: BMC Genomics 2021 22:79

    Content type: Research article

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  35. Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this s...

    Authors: Chao Yuan, Zengkui Lu, Tingting Guo, Yaojing Yue, Xijun Wang, Tianxiang Wang, Yajun Zhang, Fujun Hou, Chune Niu, Xiaopin Sun, Hongchang Zhao, Shaohua Zhu, Jianbin Liu and Bohui Yang

    Citation: BMC Genomics 2021 22:78

    Content type: Research article

    Published on:

  36. Influenza viruses are dangerous pathogens. Seventy-Seven genomes of recently emerged genotype 4 reassortant Eurasian avian-like H1N1 virus (G4-EA-H1N1) are currently available. We investigated the presence and va...

    Authors: Václav Brázda, Otília Porubiaková, Alessio Cantara, Natália Bohálová, Jan Coufal, Martin Bartas, Miroslav Fojta and Jean-Louis Mergny

    Citation: BMC Genomics 2021 22:77

    Content type: Research article

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  37. Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps wer...

    Authors: Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi, Heping Zheng, Yousong Peng and Zhongyang Tan

    Citation: BMC Genomics 2021 22:76

    Content type: Research article

    Published on:

  38. We have previously suggested that some of the mutations defining mitochondrial DNA (mtDNA) haplogroups J and K produce an uncoupling effect on oxidative phosphorylation and thus are detrimental for elite endur...

    Authors: Jukka Kiiskilä, Jari Jokelainen, Laura Kytövuori, Ilona Mikkola, Pirjo Härkönen, Sirkka Keinänen-Kiukaanniemi and Kari Majamaa

    Citation: BMC Genomics 2021 22:75

    Content type: Research article

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  39. Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a...

    Authors: Jingyu Peng, Lindsay R. Triplett and George W. Sundin

    Citation: BMC Genomics 2021 22:74

    Content type: Research article

    Published on:

  40. Although around 1% of cytosines in bees’ genomes are known to be methylated, less is known about methylation’s effect on bee behavior and fitness. Chemically altered DNA methylation levels have shown clear cha...

    Authors: María I. Pozo, Benjamin J. Hunt, Gaby Van Kemenade, Jose M. Guerra-Sanz, Felix Wäckers, Eamonn B. Mallon and Hans Jacquemyn

    Citation: BMC Genomics 2021 22:73

    Content type: Research article

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  41. Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia argut...

    Authors: Miaomiao Lin, Shihang Sun, Jinbao Fang, Xiujuan Qi, Leiming Sun, Yunpeng Zhong, Yanxiang Sun, Gu Hong, Ran Wang and Yukuo Li

    Citation: BMC Genomics 2021 22:72

    Content type: Research article

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  42. In the light of dengue being the fastest growing transmissible disease, there is a dire need to identify the mechanisms regulating the behaviour of the main vector Aedes aegypti. Disease transmission requires the...

    Authors: Sharon Rose Hill, Tanvi Taparia and Rickard Ignell

    Citation: BMC Genomics 2021 22:71

    Content type: Research article

    Published on:

  43. Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activatio...

    Authors: Ambika Dudhate, Harshraj Shinde, Pei Yu, Daisuke Tsugama, Shashi Kumar Gupta, Shenkui Liu and Tetsuo Takano

    Citation: BMC Genomics 2021 22:70

    Content type: Research article

    Published on:

  44. Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to f...

    Authors: Benjamin P. Kellman, Hratch M. Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne and Nathan E. Lewis

    Citation: BMC Genomics 2021 22:69

    Content type: Research article

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  45. Canine hip dysplasia (CHD) is a common disease, with a complex genetic background. Dogs with severe CHD sometimes also suffer from osteoarthritis (OA), an inflammatory, often painful and incurable condition. P...

    Authors: Lea Mikkola, Kaisa Kyöstilä, Jonas Donner, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2021 22:68

    Content type: Research article

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  46. Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 n...

    Authors: Hao Li, Pengfei Cui, Xue Fu, Lan Zhang, Wenjun Yan, Yaru Zhai, Changwei Lei, Hongning Wang and Xin Yang

    Citation: BMC Genomics 2021 22:67

    Content type: Research article

    Published on:

  47. Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. ...

    Authors: Tracy M. Yamawaki, Daniel R. Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang and Chi-Ming Li

    Citation: BMC Genomics 2021 22:66

    Content type: Research article

    Published on:

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