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  1. Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regu...

    Authors: Keren Long, Duo Su, Xiaokai Li, Hengkuan Li, Sha Zeng, Yu Zhang, Zhining Zhong, Yu Lin, Xuemin Li, Lu Lu, Long Jin, Jideng Ma, Qianzi Tang and Mingzhou Li
    Citation: BMC Genomics 2022 23:519
  2. Group A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and anim...

    Authors: Han Wu, Bingzhe Li, Ziping Miao, Linjie Hu, Lu Zhou and Yihan Lu
    Citation: BMC Genomics 2022 23:518
  3. Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled...

    Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, Robert D. Schnabel, Jared E. Decker and Christopher M. Seabury
    Citation: BMC Genomics 2022 23:517
  4. The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this...

    Authors: D. De Panis, H. Dopazo, E. Bongcam-Rudloff, A. Conesa and E. Hasson
    Citation: BMC Genomics 2022 23:515
  5. Ammonium is an important raw material for biomolecules and life activities, and the toxicity of ammonium is also an important ecological and agricultural issue. Ammonium toxicity in yeast has only recently bee...

    Authors: Wenhao Fu, Xiuling Cao, Tingting An, Huihui Zhao, Jie Zhang, Danqi Li, Xuejiao Jin and Beidong Liu
    Citation: BMC Genomics 2022 23:514
  6. With the emergence and spread of SARS-CoV-2 variants, genomic epidemiology and surveillance have proven invaluable tools for variant tracking. Here, we analyzed SARS-CoV-2 samples collected from personnel loca...

    Authors: Irina Maljkovic Berry, Jun Hang, Christian Fung, Yu Yang, Marcus Chibucos, Adam Pollio, Jay Gandhi, Tao Li, Matthew A. Conte, Grace M. Lidl, Jay A. Johannigman and Heather Friberg
    Citation: BMC Genomics 2022 23:513
  7. Chinese chestnut is an economically important tree species whose yield and quality are seriously affected by red spider attack. Tannins is one of the most important class secondary metabolites in plants, and i...

    Authors: Suying Li, Yanjiao Cui, Dan Liu, Zilong Zhao, Jing Zhang and Zhengli Liu
    Citation: BMC Genomics 2022 23:512
  8. Bulbus Fritillariae Cirrhosae (BFC) is an endangered high-altitude medicine and food homology plant with anti-tumor, anti-asthmatic, and antitussive activities as it contains a variety of active ingredients, espe...

    Authors: Qiuxia Lu, Rui Li, Jiaqing Liao, Yuqin Hu, Yundong Gao, Mingcheng Wang, Jian Li and Qi Zhao
    Citation: BMC Genomics 2022 23:511
  9. The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic a...

    Authors: Nadia B. Olivero, Ana S. Gonzalez-Reiche, Viviana E. Re, Gonzalo M. Castro, María B. Pisano, Paola Sicilia, María G. Barbas, Zenab Khan, Adriana van de Guchte, Jayeeta Dutta, Paulo R. Cortes, Mirelys Hernandez-Morfa, Victoria E. Zappia, Lucia Ortiz, Ginger Geiger, Daniela Rajao…
    Citation: BMC Genomics 2022 23:510
  10. Duck plague virus (DPV), belonging to herpesviruses, is a linear double-stranded DNA virus. There are many reports about the outbreak of the duck plague in a variety of countries, which caused huge economic lo...

    Authors: Ziyu Wu, Yue Zeng, Anchun Cheng, Anyang Sun, Mingshu Wang, Shun Chen, Mafeng Liu, Dekang Zhu, Xinxin Zhao, Ying Wu, Qiao Yang, Shaqiu Zhang, Juan Huang, Xumin Ou, Qun Gao, Sai Mao…
    Citation: BMC Genomics 2022 23:509
  11. The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biod...

    Authors: Brianna L. Boss, Abanoub E. Wanees, Shari J. Zaslow, Tyler G. Normile and Javier A. Izquierdo
    Citation: BMC Genomics 2022 23:508
  12. Changes in the abundance of ovarian proteins play a key role in the regulation of reproduction. However, to date, no studies have investigated such changes in pubescent goats. Herein we applied isobaric tags f...

    Authors: Ping Qin, Jing Ye, Xinbao Gong, Xu Yan, Maosen Lin, Tao Lin, Tong Liu, Hailing Li, Xiujuan Wang, Yanyun Zhu, Xiaoqian Li, Ya Liu, Yunsheng Li, Yinghui Ling, Xiaorong Zhang and Fugui Fang
    Citation: BMC Genomics 2022 23:507
  13. The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of ...

    Authors: Weian Du, Domenico Giosa, Junkang Wei, Letterio Giuffrè, Ge Shi, Lamya El Aamri, Enrico D’Alessandro, Majida Hafidi, Sybren de Hoog, Orazio Romeo and Huaiqiu Huang
    Citation: BMC Genomics 2022 23:506
  14. The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well as for evolutionary and comparative genomics. The improvement of long-read s...

    Authors: Istvan Nagy, Elisabeth Veeckman, Chang Liu, Michiel Van Bel, Klaas Vandepoele, Christian Sig Jensen, Tom Ruttink and Torben Asp
    Citation: BMC Genomics 2022 23:505
  15. The filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key ge...

    Authors: Tianxiunan Pu, Zejun Mo, Long Su, Jing Yang, Ke Wan, Linqi Wang, Renxiang Liu and Yang Liu
    Citation: BMC Genomics 2022 23:503
  16. Authors: Claude Rispe, Caroline Hervet, Nathalie de la Cotte, Romain Daveu, Karine Labadie, Benjamin Noel, Jean-Marc Aury, Steeve Thany, Emiliane Taillebois, Alison Cartereau, Anaïs Le Mauf, Claude L. Charvet, Clément Auger, Elise Courtot, Cédric Neveu and Olivier Plantard
    Citation: BMC Genomics 2022 23:502

    The original article was published in BMC Genomics 2022 23:463

  17. Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH)...

    Authors: Julie Colpitts, Philip Dunstan McLoughlin and Jocelyn Poissant
    Citation: BMC Genomics 2022 23:501
  18. The cultivated peanut (Arachis hypogaea L., AABB) is an allotetraploid hybrid between two diploid peanuts, A. duranensis (AA genome) and A. ipaensis (BB genome). Miniature inverted-repeat transposable elements (M...

    Authors: Yanyan Tang, Xiaoting Li, Changli Hu, Xiaochen Qiu, Jingjing Li, Xin Li, Hong Zhu, Jingshan Wang, Jiongming Sui and Lixian Qiao
    Citation: BMC Genomics 2022 23:500
  19. The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in...

    Authors: Kuiyin Li, Yue Fan, Guangyi Zhou, Xiaojuan Liu, Songshu Chen, Xiangcai Chang, Wenqiang Wu, Lili Duan, Maoxing Yao, Rui Wang, Zili Wang, Mingfang Yang, Yanqing Ding, Mingjian Ren, Yu Fan and Liyi Zhang
    Citation: BMC Genomics 2022 23:499
  20. The impact of S. enterica colonization in cattle is highly variable and often serovar-dependent. The aim of this study was to compare the global transcriptomes of highly pathogenic bovine-adapted S. enterica sero...

    Authors: Serajus Salaheen, Seon Woo Kim, Bradd J. Haley and Jo Ann S. Van Kessel
    Citation: BMC Genomics 2022 23:498
  21. Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it...

    Authors: Yuki Iwasaki, Toshimichi Ikemura, Kennosuke Wada, Yoshiko Wada and Takashi Abe
    Citation: BMC Genomics 2022 23:497
  22. Reliable and effective label-free quantification (LFQ) analyses are dependent not only on the method of data acquisition in the mass spectrometer, but also on the downstream data processing, including software...

    Authors: Zeeshan Hamid, Kip D. Zimmerman, Hector Guillen-Ahlers, Cun Li, Peter Nathanielsz, Laura A. Cox and Michael Olivier
    Citation: BMC Genomics 2022 23:496
  23. Shigella specie is a globally important intestinal pathogen disseminated all over the world. In this study we analyzed the genome and the proteomic component of two Shigella flexneri 2a clinical isolates, collect...

    Authors: Mónica F. Torrez Lamberti, Lucrecia C. Terán, Fabián E. Lopez, María de las Mercedes Pescaretti and Mónica A. Delgado
    Citation: BMC Genomics 2022 23:495
  24. Maternal recognition is the crucial step for establishing pregnancy in cattle. This study aims to identify endometrial genes and biological pathways involved in the maternal recognition of pregnancy. Caruncula...

    Authors: Bindu Adhikari, Chin N. Lee, Vedbar S. Khadka, Youping Deng, Glen Fukumoto, Mark Thorne, Kyle Caires, Jenee Odani and Birendra Mishra
    Citation: BMC Genomics 2022 23:494
  25. To detect changes in biological processes, samples are often studied at several time points. We examined expression data measured at different developmental stages, or more broadly, historical data. Hence, the...

    Authors: Miriam Sieg, Lina Katrin Sciesielski, Karin Michaela Kirschner and Jochen Kruppa
    Citation: BMC Genomics 2022 23:491
  26. The evolution of parasites is often directly affected by the host's environment. Studies on the evolution of the same parasites in different hosts are of great interest and are highly relevant to our understan...

    Authors: Lei Han, Tianming Lan, Yaxian Lu, Mengchao Zhou, Haimeng Li, Haorong Lu, Qing Wang, Xiuyun Li, Shan Du, Chunyu Guan, Yong Zhang, Sunil Kumar Sahu, Puyi Qian, Shaofang Zhang, Hongcheng Zhou, Wei Guo…
    Citation: BMC Genomics 2022 23:489
  27. Quaternary ammonium compound (QAC) efflux genes increase the minimum inhibitory concentration of Listeria monocytogenes (Lm) to benzalkonium chloride sanitizer, but the contribution of these genes to persistence ...

    Authors: Devin Daeschel, James B. Pettengill, Yu Wang, Yi Chen, Marc Allard and Abigail B. Snyder
    Citation: BMC Genomics 2022 23:488
  28. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) ...

    Authors: Shan Jiang, Jianfei Chen, Xiuli Li, Weike Ren, Fengxiang Li, Ting Wang, Cheng Li, Zhimin Dong, Xiangxue Tian, Li Zhang, Lili Wang, Chao lu, Jingjing Chi, Li Feng and Minghua Yan
    Citation: BMC Genomics 2022 23:486
  29. Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as da...

    Authors: Julie Boisard, Evelyne Duvernois-Berthet, Linda Duval, Joseph Schrével, Laure Guillou, Amandine Labat, Sophie Le Panse, Gérard Prensier, Loïc Ponger and Isabelle Florent
    Citation: BMC Genomics 2022 23:485
  30. Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves...

    Authors: Yanan Duan, Shurui Ma, Xuesen Chen, Xiang Shen, Chengmiao Yin and Zhiquan Mao
    Citation: BMC Genomics 2022 23:484
  31. Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 pla...

    Authors: Bingyu Ye, Wenlong Shen, Chunyan Zhang, Mengli Yu, Xinru Ding, Man Yin, Yahao Wang, Xinjie Guo, Ge Bai, Kailin Lin, Shu Shi, Ping Li, Yan Zhang, Guoying Yu and Zhihu Zhao
    Citation: BMC Genomics 2022 23:483
  32. Calliptamus italicus is a dominant species in the desert and semi-desert grassland. It is widely distributed throughout many regions such as Asia, Europe, North Africa and the Mediterranean, and has enormous dest...

    Authors: Qian Liu, Di Luo, Mengjia Wang, Xingmin Song, Xiaofang Ye, Roman Jashenko and Rong Ji
    Citation: BMC Genomics 2022 23:482
  33. Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported;...

    Authors: Jihan Li, Jingling Li, Yubo Ma, Lu Kou, Juanjuan Wei and Weixing Wang
    Citation: BMC Genomics 2022 23:481
  34. Lectin receptor-like kinases (Lec-RLKs), a subfamily of RLKs, have been demonstrated to play an important role in signal transduction from cell wall to the plasma membrane during biotic stresses. Lec-RLKs incl...

    Authors: Subhankar Biswas, Raju Mondal, Akanksha Srivastava, Maitri Trivedi, Sunil Kumar Singh and Yogesh Mishra
    Citation: BMC Genomics 2022 23:480
  35. SerpinB2 is highly expressed in immune and tumor cells and is involved in multiple biological functions, including cell survival and remodeling for disease progression. This study prepared SerpinB2-deficient m...

    Authors: Yin Ji Piao, Hoe Suk Kim, Wonshik Han and Woo Kyung Moon
    Citation: BMC Genomics 2022 23:479
  36. Calling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations ...

    Authors: Adam Nunn, Christian Otto, Mario Fasold, Peter F Stadler and David Langenberger
    Citation: BMC Genomics 2022 23:477
  37. Genome-scale metabolic network models (GEMs) provide an efficient platform for the comprehensive analysis the physical and biochemical functions of organisms due to their systematic perspective on the study of...

    Authors: Jingjing Li, Yifei Gou, Jiarui Yang, Lingxuan Zhao, Bin Wang, Tong Hao and Jinsheng Sun
    Citation: BMC Genomics 2022 23:475
  38. Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is u...

    Authors: Zhaoqin Cai, Zhipeng Cai, Jingli Huang, Aiqin Wang, Aaron Ntambiyukuri, Bimei Chen, Ganghui Zheng, Huifeng Li, Yongmei Huang, Jie Zhan, Dong Xiao and Longfei He
    Citation: BMC Genomics 2022 23:473
  39. Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coo...

    Authors: Hongwei Wang, Xiaotian Zhang, Shuangcheng Ding, Yujie Huang, Shengyong Wang, Huili Chen, Yuhang Chen and Yuting Li
    Citation: BMC Genomics 2022 23:472
  40. Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely r...

    Authors: Jiacheng Chuan, Anatoly Belov, Michel Cloutier, Xiang Li, Izhar U. H. Khan and Wen Chen
    Citation: BMC Genomics 2022 23:471
  41. Streptococcus parasuis (S. parasuis) is a close relative of Streptococcus suis (S. suis), composed of former members of S. suis serotypes 20, 22 and 26. S. parasuis could infect pigs and cows, and recently, human...

    Authors: Genglin Guo, Zhuohao Wang, Quan Li, Yanfei Yu, Yubao Li, Zhongming Tan and Wei Zhang
    Citation: BMC Genomics 2022 23:469

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