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  1. 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 Published on:

  2. 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 Published on:

  3. 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 Published on:

  4. 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:

  5. 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:

    The Correction to this article has been published in BMC Genomics 2024 25:652

  6. 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:

  7. 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:

  8. 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:

  9. 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

  10. 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:

  11. 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:

  12. 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 Published on:

  13. 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 Published on:

  14. 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 Published on:

  15. 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 Published on:

  16. 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 Published on:

  17. 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:

  18. 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 Published on:

  19. 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:

  20. 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 Published on:

  21. 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:

  22. 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 Published on:

  23. 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 Published on:

  24. 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:

  25. 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:

  26. 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 Published on:

  27. 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 Published on:

  28. 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:

  29. 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:

  30. The lesser grain borer, Rhyzopertha dominica is a serious pest of stored grains. Fumigation and contact insecticides play a major role in managing this pest globally. While insects are developing genetic resistan...

    Authors: Maria K. Sakka, Maria Riga, Panagiotis Ioannidis, Georgia V. Baliota, Martha Tselika, Rajeswaran Jagadeesan, Manoj K. Nayak, John Vontas and Christos G. Athanassiou
    Citation: BMC Genomics 2021 22:65
    Content type: Research article Published on:

  31. miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, littl...

    Authors: Jie Liu, Fuwei Li, Xin Hu, Dingguo Cao, Wei Liu, Haixia Han, Yan Zhou and Qiuxia Lei
    Citation: BMC Genomics 2021 22:64
    Content type: Research article Published on:

  32. The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang,...

    Authors: Songyue Chai, Qin Yao, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Lina Sha, Houyang Kang, Haiqin Zhang, Jun Li, Yonghong Zhou and Yi Wang
    Citation: BMC Genomics 2021 22:63
    Content type: Research article Published on:

  33. Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can int...

    Authors: Stephan Weißbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Doug Evans, Joachim Burger, Karin Everschor-Sitte, Helen Louise May-Simera and Susanne Gerber
    Citation: BMC Genomics 2021 22:62
    Content type: Research article Published on:

  34. Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutan...

    Authors: Dawei Zhang, Wenjing Wu, Xin Huang, Ke Xu, Cheng Zheng and Jin Zhang
    Citation: BMC Genomics 2021 22:61
    Content type: Research article Published on:

  35. Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the pred...

    Authors: Syed Shujaat Ali Zaidi, Masood Ur Rehman Kayani, Xuegong Zhang, Younan Ouyang and Imran Haider Shamsi
    Citation: BMC Genomics 2021 22:60
    Content type: Software Published on:

  36. We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which ha...

    Authors: Ai Sasou, Yoshikazu Yuki, Ayaka Honma, Kotomi Sugiura, Koji Kashima, Hiroko Kozuka-Hata, Masanori Nojima, Masaaki Oyama, Shiho Kurokawa, Shinichi Maruyama, Masaharu Kuroda, Shinjiro Tanoue, Narushi Takamatsu, Kohtaro Fujihashi, Eiji Goto and Hiroshi Kiyono
    Citation: BMC Genomics 2021 22:59
    Content type: Research article Published on:

  37. The mechanism of body growth in mammals is poorly understood. Here, we investigated the regulatory networks involved in body growth through transcriptomic analysis of pituitary and epiphyseal tissues of smalle...

    Authors: Jun Fang, Dong Zhang, Jun Wei Cao, Li Zhang, Chun Xia Liu, Yan Ping Xing, Feng Wang, Hong Yang Xu, Shi Chao Wang, Yu Ling, Wei Wang, Yan Ru Zhang and Huan Min Zhou
    Citation: BMC Genomics 2021 22:58
    Content type: Research article Published on:

  38. Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by ...

    Authors: Grazyella M. Yoshida and José M. Yáñez
    Citation: BMC Genomics 2021 22:57
    Content type: Research article Published on:

  39. Biological functions of biomolecules rely on the cellular compartments where they are located in cells. Importantly, RNAs are assigned in specific locations of a cell, enabling the cell to implement diverse bi...

    Authors: Hao Wang, Yijie Ding, Jijun Tang, Quan Zou and Fei Guo
    Citation: BMC Genomics 2021 22:56
    Content type: Methodology article Published on:

  40. During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic reg...

    Authors: Yingxin Zhang, Chengming Fan, Yuhong Chen, Richard R.-C. Wang, Xiangqi Zhang, Fangpu Han and Zanmin Hu
    Citation: BMC Genomics 2021 22:55
    Content type: Research article Published on:

  41. The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act a...

    Authors: Nonno Hasegawa, Maeva Techer and Alexander S. Mikheyev
    Citation: BMC Genomics 2021 22:54
    Content type: Methodology article Published on:

  42. Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known...

    Authors: Chao Yan, Yupeng Wang, Tao Lyu, Zhikang Hu, Ning Ye, Weixin Liu, Jiyuan Li, Xiaohua Yao and Hengfu Yin
    Citation: BMC Genomics 2021 22:53
    Content type: Research article Published on:

  43. Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection.

    Authors: Xiaojie Liu, Xiaoshuang Li, Xuejing Wen, Yan Zhang, Yu Ding, Yiheng Zhang, Bei Gao and Daoyuan Zhang
    Citation: BMC Genomics 2021 22:52
    Content type: Research article Published on:

  44. Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-tr...

    Authors: Ping Lin, Hui-ru Bai, Ling He, Qiu-xiang Huang, Qin-han Zeng, Yuan-zhi Pan, Bei-bei Jiang, Fan Zhang, Lei Zhang and Qing-Lin Liu
    Citation: BMC Genomics 2021 22:51
    Content type: Research article Published on:

  45. Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and...

    Authors: Peng Yu, Li Zhou, Wen-Tao Yang, Li-jun Miao, Zhi Li, Xiao-Juan Zhang, Yang Wang and Jian-Fang Gui
    Citation: BMC Genomics 2021 22:50
    Content type: Research article Published on:

  46. Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT acti...

    Authors: Shiqi Gao, Linzhi Li, Xiaolei Han, Tingting Liu, Peng Jin, Linna Cai, Miaoze Xu, Tianye Zhang, Fan Zhang, Jianping Chen, Jian Yang and Kaili Zhong
    Citation: BMC Genomics 2021 22:49
    Content type: Research article Published on:

  47. With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture....

    Authors: Jinqiang Quan, Yujun Kang, Zhicheng Luo, Guiyan Zhao, Lanlan Li and Zhe Liu
    Citation: BMC Genomics 2021 22:48
    Content type: Research article Published on:

  48. Single-cell RNA-Sequencing (scRNA-Seq) has provided single-cell level insights into complex biological processes. However, the high frequency of gene expression detection failures in scRNA-Seq data make it cha...

    Authors: Tao Cui and Tingting Wang
    Citation: BMC Genomics 2021 22:47
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:223

  49. The major pathogenesis associated with Fasciola hepatica infection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and deve...

    Authors: Krystyna Cwiklinski, Mark W. Robinson, Sheila Donnelly and John P. Dalton
    Citation: BMC Genomics 2021 22:46
    Content type: Research article Published on:

  50. Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant...

    Authors: Xiaqin Wang, Xinyang Yan, Shubin Li, Yun Jing, Lianfeng Gu, Shuangquan Zou, Jin Zhang and Bobin Liu
    Citation: BMC Genomics 2021 22:45
    Content type: Research article Published on:

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BMC Genomics

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