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  1. Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemi...

    Authors: Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Amanda de Menezes Mayer, Gabriela Bettella Cybis, Carla Andretta Moreira Neves, Patrícia Aline Gröhs Ferrareze, Meriane Demoliner, Paula Rodrigues de Almeida, Juliana Schons Gularte, Alana Witt Hansen, Matheus Nunes Weber, Juliane Deise Fleck, Ricardo Ariel Zimerman, Lívia Kmetzsch, Fernando Rosado Spilki and Claudia Elizabeth Thompson

    Citation: BMC Genomics 2021 22:371

    Content type: Research

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  2. Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a centu...

    Authors: Katie M. O’Connor, Ben J. Hayes, Craig M. Hardner, Mobashwer Alam, Robert J. Henry and Bruce L. Topp

    Citation: BMC Genomics 2021 22:370

    Content type: Research article

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  3. Systematic studies on the development and adaptation of hindlimb muscles in anura amphibians are rare. Here, we integrated analysis of transcriptome and histomorphological data for the hindlimb thigh muscle of Od...

    Authors: Yilin Shu, Jun He, Huijuan Zhang, Guangxuan Liu, Shikun Li, Shuaitao Deng and Hailong Wu

    Citation: BMC Genomics 2021 22:369

    Content type: Research article

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  4. Colonization of dairy cows by Staphylococcus aureus (S. aureus), especially those which are multi-drug resistant and toxin producing, is a concern for animal health and well-being as well as public health. The ob...

    Authors: Kruthika Patel, Sandra M. Godden, Erin E. Royster, Brian A. Crooker, Timothy J. Johnson, Emily A. Smith and Srinand Sreevatsan

    Citation: BMC Genomics 2021 22:367

    Content type: Research article

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  5. A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the ge...

    Authors: Graça Pinto, Marta Sampaio, Oscar Dias, Carina Almeida, Joana Azeredo and Hugo Oliveira

    Citation: BMC Genomics 2021 22:366

    Content type: Research article

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  6. A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome ...

    Authors: Orçun Haçariz, Charles Viau, Farial Karimian and Jianguo Xia

    Citation: BMC Genomics 2021 22:364

    Content type: Research article

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  7. Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely...

    Authors: Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch

    Citation: BMC Genomics 2021 22:363

    Content type: Research article

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  8. Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with...

    Authors: Wuhui Li, Shi Wang, Jie Hu, Chenchen Tang, Chang Wu, Junmei Liu, Li Ren, Chengfei Sun, Junjian Dong, Shaojun Liu and Xing Ye

    Citation: BMC Genomics 2021 22:362

    Content type: Research article

    Published on:

  9. Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, ...

    Authors: Min Wang, Bowei Chen, Wei Zhou, Linan Xie, Lishan Wang, Yonglan Zhang and Qingzhu Zhang

    Citation: BMC Genomics 2021 22:361

    Content type: Research

    Published on:

  10. Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a ...

    Authors: Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve-Codina, Kristina Gruden and Maria Pla

    Citation: BMC Genomics 2021 22:360

    Content type: Research article

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  11. Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of pre-RNA on tissues outside of the reproductive tract ...

    Authors: Fernando Diaz, Carson W. Allan, Therese Ann Markow, Jeremy M. Bono and Luciano M. Matzkin

    Citation: BMC Genomics 2021 22:359

    Content type: Research

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  12. Citation: BMC Genomics 2021 22:358

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2021 22:307

  13. Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is kn...

    Authors: Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka J. Lund, Asta Laiho and Laura L. Elo

    Citation: BMC Genomics 2021 22:357

    Content type: Research article

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  14. Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the Un...

    Authors: Dennis N. Lozada, Madhav Bhatta, Danise Coon and Paul W. Bosland

    Citation: BMC Genomics 2021 22:356

    Content type: Research

    Published on:

  15. Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic...

    Authors: Juncong Yan, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, Rebijith Kayattukandy Balan, Sherly George, Péter Farkas and Dongmei Li

    Citation: BMC Genomics 2021 22:355

    Content type: Research article

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  16. Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. W...

    Authors: Anna Carolina Fernandes, Vinicius Henrique da Silva, Carolina Purcell Goes, Gabriel Costa Monteiro Moreira, Thaís Fernanda Godoy, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Maurício Egídio Cantão, Mônica Corrêa Ledur, Fernanda Marcondes de Rezende and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2021 22:354

    Content type: Research article

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  17. Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the...

    Authors: Xiaowei Wang, Hongyan Hu, Zhijun Wu, Haili Fan, Guowei Wang, Tuanyao Chai and Hong Wang

    Citation: BMC Genomics 2021 22:353

    Content type: Research article

    Published on:

  18. The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family memb...

    Authors: Xiaomin Xu, Lili Zhang, Wan Zhao, Liang Fu, Yuxuan Han, Keke Wang, Luyu Yan, Ye Li, Xiao-Hong Zhang and Dong-Hong Min

    Citation: BMC Genomics 2021 22:350

    Content type: Research

    Published on:

  19. Changshun green-shell laying hens are unique to Guizhou Province, China, and have high egg quality. Improving egg production performance has become an important breeding task, and in recent years, the developm...

    Authors: Ren Mu, Yi-yin Yu, Tuya Gegen, Di Wen, Fen Wang, Zhi Chen and Wen-bin Xu

    Citation: BMC Genomics 2021 22:349

    Content type: Research

    Published on:

  20. Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar ...

    Authors: Satoshi Okubo, Kaede Terauchi, Shinji Okada, Yoshikazu Saito, Takao Yamaura, Takumi Misaka, Ken-ichiro Nakajima, Keiko Abe and Tomiko Asakura

    Citation: BMC Genomics 2021 22:347

    Content type: Research article

    Published on:

  21. Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated ...

    Authors: Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather S. Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugenia Naro-Maciel, Kathryn McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernandez, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison…

    Citation: BMC Genomics 2021 22:346

    Content type: Article

    Published on:

  22. Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and theref...

    Authors: O. Gervais, A. Barria, A. Papadopoulou, R. L. Gratacap, B. Hillestad, A. E. Tinch, S. A. M. Martin, D. Robledo and R. D. Houston

    Citation: BMC Genomics 2021 22:345

    Content type: Research

    Published on:

  23. B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their bi...

    Authors: Jordana Inácio Nascimento-Oliveira, Bruno Evaristo Almeida Fantinatti, Ivan Rodrigo Wolf, Adauto Lima Cardoso, Erica Ramos, Nathalie Rieder, Rogerio de Oliveira and Cesar Martins

    Citation: BMC Genomics 2021 22:344

    Content type: Research

    Published on:

  24. Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macropha...

    Authors: Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon and David E. MacHugh

    Citation: BMC Genomics 2021 22:343

    Content type: Research article

    Published on:

  25. Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of...

    Authors: Aliki Xanthopoulou, Javier Montero-Pau, Belén Picó, Panagiotis Boumpas, Eleni Tsaliki, Harry S. Paris, Athanasios Tsaftaris, Apostolos Kalivas, Ifigeneia Mellidou and Ioannis Ganopoulos

    Citation: BMC Genomics 2021 22:341

    Content type: Research

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  26. Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estim...

    Authors: Johannes Geibel, Christian Reimer, Torsten Pook, Steffen Weigend, Annett Weigend and Henner Simianer

    Citation: BMC Genomics 2021 22:340

    Content type: Research

    Published on:

  27. Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ant...

    Authors: José Manuel Monroy Kuhn, Karen Meusemann and Judith Korb

    Citation: BMC Genomics 2021 22:339

    Content type: Research

    Published on:

  28. Early life malnutrition is known to target adipose tissue with varying impact depending on timing of the insult. This study aimed to identify differentially expressed genes in subcutaneous (SUB) and perirenal ...

    Authors: Sharmila Ahmad, Markus Hodal Drag, Suraya Mohamad Salleh, Zexi Cai and Mette Olaf Nielsen

    Citation: BMC Genomics 2021 22:338

    Content type: Research

    Published on:

  29. Malaria control is heavily reliant on the use of insecticides that target and kill the adult female Anopheline vector. The intensive use of insecticides of the pyrethroid class has led to widespread resistance...

    Authors: V. A. Ingham, F. Brown and H. Ranson

    Citation: BMC Genomics 2021 22:337

    Content type: Research article

    Published on:

  30. Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerab...

    Authors: Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh and Soumyadeep Nandi

    Citation: BMC Genomics 2021 22:336

    Content type: Research article

    Published on:

  31. Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs wi...

    Authors: Zhenyang Liao, Xunxiao Zhang, Shengcheng Zhang, Zhicong Lin, Xingtan Zhang and Ray Ming

    Citation: BMC Genomics 2021 22:335

    Content type: Research

    Published on:

  32. Feeding behavior traits are an essential part of livestock production. However, the genetic base of feeding behavior traits remains unclear in Pekin ducks. This study aimed to determine novel loci related to f...

    Authors: Guang-Sheng Li, Feng Zhu, Fan Zhang, Fang-Xi Yang, Jin-Ping Hao and Zhuo-Cheng Hou

    Citation: BMC Genomics 2021 22:334

    Content type: Research

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  33. Sclerotinia sclerotiorum, the cause of Sclerotinia stem rot (SSR), is a host generalist necrotrophic fungus that can cause major yield losses in chickpea (Cicer arietinum) production. This study used RNA sequenci...

    Authors: Virginia W. Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis and Mark C. Derbyshire

    Citation: BMC Genomics 2021 22:333

    Content type: Research

    Published on:

  34. In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not...

    Authors: Yibin Qiu, Rongrong Ding, Zhanwei Zhuang, Jie Wu, Ming Yang, Shenping Zhou, Yong Ye, Qian Geng, Zheng Xu, Sixiu Huang, Gengyuan Cai, Zhenfang Wu and Jie Yang

    Citation: BMC Genomics 2021 22:332

    Content type: Research article

    Published on:

  35. Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves inv...

    Authors: Xuzixin Zhou, Yanbin Xue, Meiqin Mao, Yehua He, Mark Owusu Adjei, Wei Yang, Hao Hu, Jiawen Liu, Lijun Feng, Huiling Zhang, Jiaheng Luo, Xi Li, Lingxia Sun, Zhuo Huang and Jun Ma

    Citation: BMC Genomics 2021 22:331

    Content type: Research article

    Published on:

  36. The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At...

    Authors: Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang and Jun Zhang

    Citation: BMC Genomics 2021 22:329

    Content type: Research article

    Published on:

  37. Fatty liver has become a main problem that causes huge economic losses in many aquaculture modes. It is a common physiological or pathological phenomenon in aquaculture, but the causes and occurring mechanism ...

    Authors: Xiao-Juan Zhang, Li Zhou, Wei-Jia Lu, Wen-Xuan Du, Xiang-Yuan Mi, Zhi Li, Xi-Yin Li, Zhong-Wei Wang, Yang Wang, Ming Duan and Jian-Fang Gui

    Citation: BMC Genomics 2021 22:328

    Content type: Research

    Published on:

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

    Authors: Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni, Ioannis P. Trougakos, Dafni-Eleftheria Pefani, Eric O’Neill, Sarantis Gagos…

    Citation: BMC Genomics 2021 22:327

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2018 19:37

  39. The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been...

    Authors: Braham Dhillon, Richard C. Hamelin and Jeffrey A. Rollins

    Citation: BMC Genomics 2021 22:326

    Content type: Research article

    Published on:

  40. Mitochondrial genome has aseries of characteristics such as simple structure, no recombination, maternalinheritance, stable structure, fast evolution rate, and high copy number. Moreover, it is easy to be sequ...

    Authors: Xingdong Wang, Jie Pei, Pengjia Bao, Mengli Cao, Shaoke Guo, Rende Song, Weiru Song, Chunnian Liang, Ping Yan and Xian Guo

    Citation: BMC Genomics 2021 22:325

    Content type: Research

    Published on:

  41. Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a ...

    Authors: Axel Orban, Annsophie Weber, Robert Herzog, Florian Hennicke and Martin Rühl

    Citation: BMC Genomics 2021 22:324

    Content type: Research

    Published on:

  42. Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small v...

    Authors: Karina Brinkrolf, Shantanu P. Shukla, Sven Griep, Oliver Rupp, Philipp Heise, Alexander Goesmann, David G. Heckel, Heiko Vogel and Andreas Vilcinskas

    Citation: BMC Genomics 2021 22:323

    Content type: Research article

    Published on:

  43. RNA sequencing analysis focus on the detection of differential gene expression changes that meet a two-fold minimum change between groups. The variability present in RNA sequencing data may obscure the detecti...

    Authors: William W. Wilfinger, Robert Miller, Hamid R. Eghbalnia, Karol Mackey and Piotr Chomczynski

    Citation: BMC Genomics 2021 22:322

    Content type: Methodology article

    Published on:

  44. Birth weight (BW) is one of the most widely studied anthropometric traits in humans because of its role in various adult-onset diseases. The number of loci associated with BW has increased dramatically since t...

    Authors: William R. P. Denault, Julia Romanowska, Øyvind Helgeland, Bo Jacobsson, Håkon K. Gjessing and Astanand Jugessur

    Citation: BMC Genomics 2021 22:321

    Content type: Research article

    Published on:

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