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  1. Single-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many sc...

    Authors: Xinlei Wang, Lei Yu and Angela Ruohao Wu

    Citation: BMC Genomics 2021 22:420

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:554

  2. Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal p...

    Authors: Yu Du, Yong Wang, Qing Xu, Jiangjiang Zhu and Yaqiu Lin

    Citation: BMC Genomics 2021 22:417

    Content type: Research

    Published on:

  3. Copper was used for many years in aquaculture operations as an effective algaecide or a parasite treatment of fish. It is an essential nutrient with numerous functions in organisms, but is toxic at high concen...

    Authors: Wenjie Jin, Zixuan Li, Fengxia Ran, Shen Huang, Kefan Huo, Jianjuan Li, Qingshuo Han, Guojie Wang, Zhenji Wang, Shenlong Jian, Kemao Li and Changzhong Li

    Citation: BMC Genomics 2021 22:416

    Content type: Research article

    Published on:

  4. Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multipl...

    Authors: Danny Bergeron, Cédric Laforest, Stacey Carpentier, Annabelle Calvé, Étienne Fafard-Couture, Gabrielle Deschamps-Francoeur and Michelle S. Scott

    Citation: BMC Genomics 2021 22:414

    Content type: Research

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  5. The spleen is the largest secondary lymphoid organ and the main site where stress erythropoiesis occurs. It is known that hypoxia triggers the expansion of erythroid progenitors; however, its effects on spleni...

    Authors: Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiangwen Chi and Tongzuo Zhang

    Citation: BMC Genomics 2021 22:413

    Content type: Research

    Published on:

  6. The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emergin...

    Authors: Sébastien Riquier, Marc Mathieu, Chloé Bessiere, Anthony Boureux, Florence Ruffle, Jean-Marc Lemaitre, Farida Djouad, Nicolas Gilbert and Thérèse Commes

    Citation: BMC Genomics 2021 22:412

    Content type: Research article

    Published on:

  7. Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans and the handling or consumption of contaminated poultry meat is a key source of infection. Selective breeding of poultry that exhib...

    Authors: Kay M. Russell, Jacqueline Smith, Abi Bremner, Cosmin Chintoan-Uta, Lonneke Vervelde, Androniki Psifidi and Mark P. Stevens

    Citation: BMC Genomics 2021 22:411

    Content type: Research

    Published on:

  8. Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unkn...

    Authors: Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou and Yun Zheng

    Citation: BMC Genomics 2021 22(Suppl 3):405

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  9. Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimat...

    Authors: Lily D. Peck, Reuben W. Nowell, Julie Flood, Matthew J. Ryan and Timothy G. Barraclough

    Citation: BMC Genomics 2021 22:404

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:514

  10. There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic difference...

    Authors: Ruijie Liu, Rick Tearle, Wai Yee Low, Tong Chen, Dana Thomsen, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams

    Citation: BMC Genomics 2021 22:410

    Content type: Research

    Published on:

  11. Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development a...

    Authors: Vittoria Roncalli, Matthew C. Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline and Petra H. Lenz

    Citation: BMC Genomics 2021 22:409

    Content type: Research article

    Published on:

  12. Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature w...

    Authors: Dessie Salilew-Wondim, Dawit Tesfaye, Franca Rings, Eva Held-Hoelker, Dennis Miskel, Marc-Andre Sirard, Ernst Tholen, Karl Schellander and Michael Hoelker

    Citation: BMC Genomics 2021 22:408

    Content type: Research

    Published on:

  13. Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretati...

    Authors: Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S. Cram and Yu Zhang

    Citation: BMC Genomics 2021 22:407

    Content type: Software

    Published on:

  14. Chlamydia psittaci is an avian pathogen that can cause lethal human infections. Diagnosis of C. psittaci pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic tech...

    Authors: Kaiying Wang, Xiong Liu, Huiying Liu, Peihan Li, Yanfeng Lin, Dongdong Yin, Lang Yang, Jinhui Li, Shenlong Li, Leili Jia, Changqing Bai, Yongqiang Jiang, Peng Li and Hongbin Song

    Citation: BMC Genomics 2021 22:406

    Content type: Research article

    Published on:

  15. The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as An...

    Authors: So-Ra Han, Byeollee Kim, Jong Hwa Jang, Hyun Park and Tae-Jin Oh

    Citation: BMC Genomics 2021 22:403

    Content type: Research

    Published on:

  16. Observational studies have identified various associations between neuroimaging alterations and neuropsychiatric disorders. However, whether such associations could truly reflect causal relations remains still...

    Authors: Weichen Song, Wei Qian, Weidi Wang, Shunying Yu and Guan Ning Lin

    Citation: BMC Genomics 2021 22(Suppl 3):342

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  17. Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characte...

    Authors: Noah DeWitt, Mohammed Guedira, Edwin Lauer, J. Paul Murphy, David Marshall, Mohamed Mergoum, Jerry Johnson, James B. Holland and Gina Brown-Guedira

    Citation: BMC Genomics 2021 22:402

    Content type: Research article

    Published on:

  18. Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed w...

    Authors: Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Jinping Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang and Lizhi Lu

    Citation: BMC Genomics 2021 22:401

    Content type: Research article

    Published on:

  19. Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment an...

    Authors: Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer and Rita V. M. Rio

    Citation: BMC Genomics 2021 22:400

    Content type: Research article

    Published on:

  20. Pair bonding with a reproductive partner is rare among mammals but is an important feature of human social behavior. Decades of research on monogamous prairie voles (Microtus ochrogaster), along with comparative ...

    Authors: Joel A. Tripp, Alejandro Berrio, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young and Steven M. Phelps

    Citation: BMC Genomics 2021 22:399

    Content type: Research

    Published on:

  21. A conformational epitope (CE) is composed of neighboring amino acid residues located on an antigenic protein surface structure. CEs bind their complementary paratopes in B-cell receptors and/or antibodies. An ...

    Authors: Ying-Tsang Lo, Tao-Chuan Shih, Tun-Wen Pai, Li-Ping Ho, Jen-Leih Wu and Hsin-Yiu Chou

    Citation: BMC Genomics 2021 22(Suppl 2):116

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  22. Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled...

    Authors: Wilson Nandolo, Gábor Mészáros, Maria Wurzinger, Liveness J. Banda, Timothy N. Gondwe, Henry A. Mulindwa, Helen N. Nakimbugwe, Emily L. Clark, M. Jennifer Woodward-Greene, Mei Liu, George E. Liu, Curtis P. Van Tassell, Benjamin D. Rosen and Johann Sölkner

    Citation: BMC Genomics 2021 22:398

    Content type: Research article

    Published on:

  23. Chromosomes are organized into units called topologically associated domains (TADs). TADs dictate regulatory landscapes and other DNA-dependent processes. Even though various factors that contribute to the spe...

    Authors: Benjamin Soibam and Ayzhamal Zhamangaraeva

    Citation: BMC Genomics 2021 22:397

    Content type: Research

    Published on:

  24. Transmission of pathogens by vector mosquitoes is intrinsically linked with mosquito’s reproductive strategy because anautogenous mosquitoes require vertebrate blood to develop a batch of eggs. Each cycle of e...

    Authors: Dilip K. Nag, Constentin Dieme, Pascal Lapierre, Erica Lasek-Nesselquist and Laura D. Kramer

    Citation: BMC Genomics 2021 22:396

    Content type: Research article

    Published on:

  25. Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited.

    Authors: Jieyin Zhao, Peng Wang, Wenju Gao, Yilei Long, Yuxiang Wang, Shiwei Geng, Xuening Su, Yang Jiao, Quanjia Chen and Yanying Qu

    Citation: BMC Genomics 2021 22:395

    Content type: Research article

    Published on:

  26. The pine wood nematode Bursaphelenchus xylophilus is a destructive pest of Pinus trees worldwide and lacks effective control measures. Screening for nematotoxic proteins has been undertaken to develop new strateg...

    Authors: Ye Chen, Xiang Zhou, Kai Guo, Sha-Ni Chen and Xiu Su

    Citation: BMC Genomics 2021 22:394

    Content type: Research

    Published on:

  27. Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of...

    Authors: Sonali Sachin Ranade and Ulrika Egertsdotter

    Citation: BMC Genomics 2021 22:392

    Content type: Research

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:515

  28. Spodoptera frugiperda is a serious pest that causes devastating losses to many major crops, including corn, rice, sugarcane, and peanut. Camptothecin (CPT) is a bioactive secondary metabolite of the woody plant C...

    Authors: Benshui Shu, Yan Zou, Haikuo Yu, Wanying Zhang, Xiangli Li, Liang Cao and Jintian Lin

    Citation: BMC Genomics 2021 22:391

    Content type: Research article

    Published on:

  29. Intron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi,...

    Authors: Georg Back and Dirk Walther

    Citation: BMC Genomics 2021 22:390

    Content type: Research

    Published on:

  30. Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of...

    Authors: Seth Commichaux, Kiran Javkar, Padmini Ramachandran, Niranjan Nagarajan, Denis Bertrand, Yi Chen, Elizabeth Reed, Narjol Gonzalez-Escalona, Errol Strain, Hugh Rand, Mihai Pop and Andrea Ottesen

    Citation: BMC Genomics 2021 22:389

    Content type: Research article

    Published on:

  31. Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors ...

    Authors: Li Liu, Zhen Wang, Yingjuan Su and Ting Wang

    Citation: BMC Genomics 2021 22:388

    Content type: Research article

    Published on:

  32. The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk ...

    Authors: Xiaolei Zhang, Ming Lu, Aiai Xia, Tao Xu, Zhenhai Cui, Ruiying Zhang, Wenguo Liu and Yan He

    Citation: BMC Genomics 2021 22:386

    Content type: Research

    Published on:

  33. Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with the M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for it...

    Authors: Fernanda Cornejo-Granados, Thomas A. Kohl, Flor Vásquez Sotomayor, Sönke Andres, Rogelio Hernández-Pando, Juan Manuel Hurtado-Ramirez, Christian Utpatel, Stefan Niemann, Florian P. Maurer and Adrian Ochoa-Leyva

    Citation: BMC Genomics 2021 22:385

    Content type: Research

    Published on:

  34. Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-le...

    Authors: Yu-Fu Gao, Dong-Hui Zhao, Jia-Qi Zhang, Jia-Shuo Chen, Jia-Lin Li, Zhuo Weng and Li-Ping Rong

    Citation: BMC Genomics 2021 22:383

    Content type: Research article

    Published on:

  35. The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was fir...

    Authors: Stefania Bertazzoni, Darcy A. B. Jones, Huyen T. Phan, Kar-Chun Tan and James K. Hane

    Citation: BMC Genomics 2021 22:382

    Content type: Research article

    Published on:

  36. Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal th...

    Authors: Yang Xi, Qian Xu, Qin Huang, Shengchao Ma, Yushi Wang, Chunchun Han, Rongping Zhang, Jiwen Wang, Hehe Liu and Liang Li

    Citation: BMC Genomics 2021 22:381

    Content type: Research

    Published on:

  37. Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array ...

    Authors: Kimberly R. Andrews, Samuel S. Hunter, Brandi K. Torrevillas, Nora Céspedes, Sarah M. Garrison, Jessica Strickland, Delaney Wagers, Gretchen Hansten, Daniel D. New, Matthew W. Fagnan and Shirley Luckhart

    Citation: BMC Genomics 2021 22:378

    Content type: Methodology article

    Published on:

  38. Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pre...

    Authors: Katharina S. Weber, Karen Wagener, Miguel Blanco, Stefan Bauersachs and Heinrich Bollwein

    Citation: BMC Genomics 2021 22:377

    Content type: Research article

    Published on:

  39. The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, g...

    Authors: Ningyawen Liu, Lu Zhang, Yanli Zhou, Mengling Tu, Zhenzhen Wu, Daping Gui, Yongpeng Ma, Jihua Wang and Chengjun Zhang

    Citation: BMC Genomics 2021 22:376

    Content type: Database

    Published on:

  40. Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, li...

    Authors: Hongmei Yuan, Wendong Guo, Lijuan Zhao, Ying Yu, Si Chen, Lei Tao, Lili Cheng, Qinghua Kang, Xixia Song, Jianzhong Wu, Yubo Yao, Wengong Huang, Ying Wu, Yan Liu, Xue Yang and Guangwen Wu

    Citation: BMC Genomics 2021 22:375

    Content type: Research article

    Published on:

  41. 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is in...

    Authors: Huili Qiao, Jingya Wang, Yuanzhuo Wang, Juanjuan Yang, Bofan Wei, Miaomiao Li, Bo Wang, Xiaozhe Li, Yang Cao, Ling Tian, Dandan Li, Lunguang Yao and Yunchao Kan

    Citation: BMC Genomics 2021 22:374

    Content type: Research

    Published on:

  42. Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent pr...

    Authors: Rachel Rattner, Shree Prasad Thapa, Tyler Dang, Fatima Osman, Vijayanandraj Selvaraj, Yogita Maheshwari, Deborah Pagliaccia, Andres S. Espindola, Subhas Hajeri, Jianchi Chen, Gitta Coaker, Georgios Vidalakis and Raymond Yokomi

    Citation: BMC Genomics 2021 22:373

    Content type: Research article

    Published on:

  43. Phytophthora capsici root rot (PRR) is a disastrous disease in peppers (Capsicum spp.) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wiltin...

    Authors: Jin-Song Du, Lin-Feng Hang, Qian Hao, Hai-Tao Yang, Siyad Ali, Radwa Salah Ezaat Badawy, Xiao-Yu Xu, Hua-Qiang Tan, Li-Hong Su, Huan-Xiu Li, Kai-Xi Zou, Yu Li, Bo Sun, Li-Jin Lin and Yun-Song Lai

    Citation: BMC Genomics 2021 22:372

    Content type: Research

    Published on:

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