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  1. DNA methylation plays a crucial role in species development and environmental adaptation. In mammals, there are significant dietary changes from infancy to adulthood. Notably, the red panda transitions from mi...

    Authors: Lei Chen, Liang Zhang, Yanni Zhao, Ming He, Honglin Wu, Jingheng Wang, Zhoulong Chen, Yongqi Zhao, Fujun Shen and Xiuyue Zhang
    Citation: BMC Genomics 2025 26:404
    Content type: Research Published on:

  2. WRKY transcription factors play a vital role in regulating plant growth, development, and secondary metabolism. Tripterygium wilfordii is a medicinal plant that has been widely utilized in rheumatoid arthritis th...

    Authors: Limei Tang, Xinyu Qi, Jiayu Chen, Yujun Zhao, Junhao Gu, Shanshan Zhu, Wei Gao and Lichan Tu
    Citation: BMC Genomics 2025 26:403
    Content type: Research Published on:

  3. Transient receptor potential (TRP) ion channels play crucial roles in mediating responses to environmental stimuli, as well as regulating homeostasis and developmental processes in insects. Several members of ...

    Authors: Hongai Su, Qianxuan Dai, Feiyue Teng, Ziyuan Li, Yixiang Qi and Yongyue Lu
    Citation: BMC Genomics 2025 26:401
    Content type: Research Published on:

  4. Whole-genome sequencing using high-throughput sequencing is essential for identifying and characterising chromosomes and plasmids in nosocomial and environmental bacterial pathogens, including those with biote...

    Authors: Bertrand Bearzatto, Jean-François Durant, Jérôme Ambroise and Jean-Luc Gala
    Citation: BMC Genomics 2025 26:396
    Content type: Research Published on:

  5. Influenza A virus (IAV) is a major global health threat, causing seasonal epidemics and occasional pandemics. Particularly, Influenza A viruses from avian species pose significant zoonotic threats, with PB2 ad...

    Authors: Sangwook Kim, Min-Ah Kim, Bitgoeul Kim, Jisu Lee, Se-Kyung Jung, Jonghong Kim, Ho-Young Chung, Chung-Young Lee and Sungmoon Jeong
    Citation: BMC Genomics 2025 26:395
    Content type: Research Published on:

  6. Investigating bacterial methylation profiles provides essential complementary information to the native DNA sequence, significantly extending our understanding of how DNA modifications influence virulence, ant...

    Authors: Valentina Galeone, Johanna Dabernig-Heinz, Mara Lohde, Christian Brandt, Christian Kohler, Gabriel E. Wagner and Martin Hölzer
    Citation: BMC Genomics 2025 26:394
    Content type: Research Published on:

  8. Transcriptomic benchmark concentration (BMC) modeling provides quantitative toxicogenomic information that is increasingly being used in regulatory risk assessment of data poor chemicals. Over the past decade,...

    Authors: Xiugong Gao, Miranda R. Yourick, Kayla Campasino, Yang Zhao, Estatira Sepehr, Cory Vaught, Robert L. Sprando and Jeffrey J. Yourick
    Citation: BMC Genomics 2025 26:392
    Content type: Research Published on:

  9. InDels are the most common type of length polymorphism and play a critical role in the genetic traits of many important phenotypes in both plants and animals, making them an ideal source for length polymorphis...

    Authors: Jinchang Yang, Pengxu Meng, Hang Mi, Xueying Wang, Jin Yang, Shaohong Fu, Wanzhuo Gong, Ruifan Bao, Wujiao Deng, Haimei Wu, Zhiqin Liu, Sijia Yang, Jixing Ni, Jian Liu and Haoran Shi
    Citation: BMC Genomics 2025 26:391
    Content type: Research Published on:

  10. Rust fungi are destructive pathogens in crop plants, having led to epidemics and damaging crops all over the world. The rust Puccinia silphii (Basidiomycota) infects Silphium integrifolium, which is a member of t...

    Authors: Jacqueline S. de Mattos, Kyle Keepers, Peter A. Innes, Clifton P. Bueno de Mesquita, C. Alisha Quandt, Nolan C. Kane, Yaniv Brandvain and Kathryn Turner
    Citation: BMC Genomics 2025 26:390
    Content type: Research Published on:

  11. The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-free (AF) methods offer a scal...

    Authors: Daniel J. van Zyl, Marcel Dunaiski, Houriiyah Tegally, Cheryl Baxter, Tulio de Oliveira and Joicymara S. Xavier
    Citation: BMC Genomics 2025 26:389
    Content type: Research Published on:

  12. Long read sequencing technologies provide an efficient approach to generating highly contiguous and informative assemblies. However, higher relative error rates can introduce frameshifts and premature stop cod...

    Authors: Janet S.H. Lorv and Brendan J. McConkey
    Citation: BMC Genomics 2025 26:388
    Content type: Software Published on:

  13. Despite the presence of a large number of toxic components, primarily juglone, in walnut green husks, these components have failed to prevent infestations of the specialized pest Atrijuglans aristata. At present,...

    Authors: Dan-dan Feng, Cai-qing Yang, Michael C. Orr and Ai-bing Zhang
    Citation: BMC Genomics 2025 26:387
    Content type: Research Published on:

  14. Most habitats on Earth house unfathomable microbial diversity, yet much of it remains uncultured. The same applies to temperate phages, most of which documented to date are predicted purely in silico from the ...

    Authors: Nikita Zrelovs, Karina Svanberga, Juris Jansons, Kristaps Lamsters, Janis Karuss, Maris Krievans, Davids Fridmanis, Andris Dislers and Andris Kazaks
    Citation: BMC Genomics 2025 26:386
    Content type: Research Published on:

  15. Hypoxia often has negative effects on testis development and spermatogenesis of mammals. Plateau yaks have lived in the hypoxia environment for generations, but have ensured testicular function, which is close...

    Authors: Rui MA, Yan CUI, Si-Jiu YU, Yang-Yang PAN, Jun-feng HE, Ya-ying WANG, Jing-lei WANG, Xiao-yan WANG, Xue-feng BAI, Hui ZHANG, Shan-shan YANG and Qian ZHANG
    Citation: BMC Genomics 2025 26:385
    Content type: Research Published on:

  16. Artemisia argyi, a significant medicinal plant in China, is known for its high content of essential oils, flavonoids, and other bioactive compounds. MYB transcription factors are the largest gene family in plants...

    Authors: Sainan Peng, Qianwen Zhang, Yun Yang, Yukun Li, Wunian Feng, Dan Zhao, Bisheng Huang, Dahui Liu and Yuhuan Miao
    Citation: BMC Genomics 2025 26:384
    Content type: Research Published on:

  17. The Pyrabactin resistance 1-like proteins (PYR/PYL/RCAR) protein plays a critical regulatory role in the ABA signal transduction pathway as a direct receptor of abscisic acid (ABA). Although PYL genes have bee...

    Authors: Kun Wang, Jiao Cheng, Jing-Ru Chen, Yan-Yan Luo, Yu-Heng Yao and Li-Li Nan
    Citation: BMC Genomics 2025 26:383
    Content type: Research Published on:

  18. Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at ...

    Authors: Francesca Bini, Irene Soffritti, Maria D’Accolti, Eleonora Mazziga, Julio Diaz Caballero, Sophia David, Silvia Argimon, David M. Aanensen, Antonella Volta, Matteo Bisi, Sante Mazzacane and Elisabetta Caselli
    Citation: BMC Genomics 2025 26:382
    Content type: Research Published on:

  19. Copy number variations (CNVs) are an important source of genomic variation that play an active role in modulating biological processes by altering gene expression and dosage. These structural variants involve ...

    Authors: Giovanni C. Ladeira, Pablo J. Pinedo, José E. P. Santos, William W. Thatcher and Fernanda M. Rezende
    Citation: BMC Genomics 2025 26:381
    Content type: Research Published on:

  20. Takifugu rubripes is an economically valuable fish species in Asia. The implementation of all-male culture for T. rubripes is highly anticipated in aquaculture. Aromatase inhibitor (AI, letrozole) treatment was f...

    Authors: Xufang Shen, Hongwei Yan, Mingtao Hu, Huiting Zhou, Qi Zhang, Rui Gao, Qi Liu and Qunwen Sun
    Citation: BMC Genomics 2025 26:380
    Content type: Research Published on:

  21. Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements of phenotypes like meat quality, methane emission, and disease suscep...

    Authors: Ruwaa I. Mohamed, Taylor B. Ault-Seay, Sonia J. Moisá, Jonathan E. Beever, Agustín G. Ríus and Troy N. Rowan
    Citation: BMC Genomics 2025 26:379
    Content type: Research Published on:

  22. The medicinal mushroom Sanghuangporus is renowned in East Asia for its potent therapeutic properties, attributed in part to its bioactive sesquiterpenoids. However, despite their recognized medicinal potential, t...

    Authors: Yoonhee Cho, Chang Wan Seo, Hyeonjae Cho, Yeongwoon Jin, Abel Severin Lupala, Sang Hee Shim and Young Woon Lim
    Citation: BMC Genomics 2025 26:378
    Content type: Research Published on:

  23. In the genetic breeding research of dairy goats, traditional genotyping methods have limitations, and existing goat chips have shortcomings in functional loci and other aspects, which cannot meet the precise g...

    Authors: Jianqing Zhao, Yaling Wang, Jiayidaer Kamalibieke, Ping Gong, Fuhong Zhang, Huaiping Shi, Wei Wang and Jun Luo
    Citation: BMC Genomics 2025 26:377
    Content type: Research Published on:

  24. Peanut (Arachis hypogaea L., 2n = 2x = 20) is an important industrial and oil crop that is widely grown in more than 100 countries. In recent years, breeders have focused on increasing the seed number per pod to ...

    Authors: Long Li, Shunli Cui, Xiukun Li, Mingyu Hou, Yingru Liu and Lifeng Liu
    Citation: BMC Genomics 2025 26:376
    Content type: Research Published on:

  25. Strong tolerance to seed aging is an important agricultural trait for sweet corn production. Previous studies have primarily focused on the QTLs for the seed vigor. However, there were few researches involving...

    Authors: Zili Zhang, Ruichun Yang, Lei Gao, Shilin Huang, Feng Jiang, Qingchun Chen, Pengfei Liu and Faqiang Feng
    Citation: BMC Genomics 2025 26:375
    Content type: Research Published on:

  26. Campylobacter jejuni (C. jejuni), is a leading cause of food-borne pathogen, poses significant threats to poultry industry and public health. Post-transcriptional modifications play crucial roles in regulating th...

    Authors: Yanan Zhao, Yuanmei Wang, Yanru Ren, Long Liu, Tianyi Wang, Liying Liu and Xianyao Li
    Citation: BMC Genomics 2025 26:374
    Content type: Research Published on:

  27. The light environment significantly influences crop growth, development, quality, and yield, particularly in controlled-environment agriculture. Recent advances in artificial lighting technology have allowed g...

    Authors: Kangni Zhang, Lina Wei, Jingpeng Geng, Weimin Zhan, Yankun Li, Yong Shi, Yanpei Zhang, Shizhan Chen and Jianping Yang
    Citation: BMC Genomics 2025 26:373
    Content type: Research Published on:

  28. Various studies have highlighted significant differences in developmental kinetics and sensitivity to developmental conditions between male and female bovine embryos. These differences are thought to be caused...

    Authors: Dessie Salilew-Wondim, Ernst Tholen, Christine Große-Brinkhaus, Eva Held-Hoelker, Dennis Miskel, Franca Rings, Karl Schellander, Urban Besenfelder, Vitezslav Havlicek, Dawit Tesfaye and Michael Hoelker
    Citation: BMC Genomics 2025 26:372
    Content type: Research Published on:

  29. The poultry industry in sub-Saharan Africa is a rapidly developing sector mostly based on smallholder farming. Increased demand for poultry-derived products, driven by the growing economy and population, has i...

    Authors: Georgios Banos, Mekonnen Girma, Bersabhe Solomon, Pourya Davoudi, Wondmeneh Esatu, Tadelle Dessie, Androniki Psifidi, Kellie Watson, Olivier Hanotte and Enrique Sánchez-Molano
    Citation: BMC Genomics 2025 26:371
    Content type: Research Published on:

  30. Plant responses to biotic and abiotic stresses are complex processes. Previous studies have shown that the LBD gene family plays important roles in plant growth and development as well as in plant defense against...

    Authors: Wenqiang Dai, Yaoling Li, Zhenghan Chen, Fuqiang He, Hui Wang, Jiali Peng, Kai Liu, Hongxia Wang, Xiuhong An and Shugang Zhao
    Citation: BMC Genomics 2025 26:370
    Content type: Research Published on:

  31. Human adenovirus (HAdV) infection can cause high fever, pneumonia, and even death, posing a serious threat to human health. This study analyzes the epidemiological characteristics and genetic features of respi...

    Authors: Huixin Dou, Chunmei Chen, Tongyun Song, Xu Sun, Feifei He, Yongjian Jia, Xiaoyu Wang, Yajuan Jiang, Ying Yue, Shiqing Huang, ShiGan Yan, Boyan Jiao and Baihai Jiao
    Citation: BMC Genomics 2025 26:369
    Content type: Research Published on:

  32. The soil amoeba Acanthamoeba castellanii is an emerging model organism with which to study a wide range of biomedical, microbiological, and evolutionary phenomena. While transformation systems were established fo...

    Authors: Morgan J. Colp, Cédric Blais, Bruce A. Curtis and John M. Archibald
    Citation: BMC Genomics 2025 26:368
    Content type: Research Published on:

  34. The HD-Zip family of plant-specific transcription factors coordinates developmental processes and abiotic stress adaptation, including drought tolerance in bioenergy crops such as physic nut. Although HD-Zip p...

    Authors: Yuehui Tang, Xiaohui Wang, Yaoyao Wang, Jiatong Xie, Ruoyu Zhang, Tengfei Liu, Sainan Jia and Xinxin Bao
    Citation: BMC Genomics 2025 26:366
    Content type: Research Published on:

  35. Diapause is a crucial adaptive strategy employed across numerous insect species, endowing them to survive in unfavorable environments. Helicoverpa armigera, one of the most destructive pests globally, undergoes d...

    Authors: Zhaohong Ni, Yan Li, Shunchao Xia, Zhaolang Teng, Jianjun Guo, Jing Liao and Haiyin Li
    Citation: BMC Genomics 2025 26:365
    Content type: Research Published on:

  36. Population genomic analysis can reconstruct the phylogenetic relationship and demographic history, and identify genomic selective signatures of a species. To date, fundamental aspects of population genomic ana...

    Authors: Huamiao Liu, Bo Zhu, Tianjiao Wang, Yimeng Dong, Yan Ju, Yang Li, Weilin Su, Ranran Zhang, Shiwu Dong, Hongliang Wang, Yongna Zhou, Yanmin Zhu, Lei Wang, Zhengyi Zhang, Pei Zhao, Shuyan Zhang…
    Citation: BMC Genomics 2025 26:364
    Content type: Research Published on:

  37. Domains can be viewed as portable units of protein structure, folding, function, evolution, and design. Small proteins are often found to be composed of only a single domain, while most large proteins consist ...

    Authors: Jingpu Zhang, Lianping Deng and Lei Deng
    Citation: BMC Genomics 2025 23(Suppl 6):869
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 6

  38. Global climate change has significantly increased environmental stress in marine ecosystems, with rising sea surface temperatures and declining dissolved oxygen (DO) levels. These stressors pose critical chall...

    Authors: Qiang Wang, Shuqing Zhang, Xiaohua He, Siyi Li, Xiaohui Xu, Yanwei Feng, Jianmin Yang and Guohua Sun
    Citation: BMC Genomics 2025 26:363
    Content type: Research Published on:

  39. Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previou...

    Authors: Michael Landi, Anna Vittoria Carluccio, Trushar Shah, Adnan Niazi, Livia Stavolone, Laurent Falquet, Andreas Gisel and Erik Bongcam-Rudloff
    Citation: BMC Genomics 2025 26:362
    Content type: Research Published on:

  40. Mycoplasma bovis is a prominent pathogen associated with respiratory disease in livestock. Respiratory disease in cattle often involves co-infection, where a primary viral infection can weaken the host immune sys...

    Authors: Anna K. Goldkamp, Randy G. Atchison, Shollie M. Falkenberg, Rohana P. Dassanayake, John D. Neill and Eduardo Casas
    Citation: BMC Genomics 2025 26:361
    Content type: Research Published on:

  41. Plasma proteins, especially immune-related proteins, are vital for assessing immune health and predicting disease risks. Despite their significance, the link between these proteins and systemic immune function...

    Authors: Min Zhang, Nan Xu, Qi Cheng, Jing Ye, Shiwei Wu, Haoliang Liu, Chengkui Zhao, Lei Yu and Weixing Feng
    Citation: BMC Genomics 2025 26:360
    Content type: Software Published on:

  42. This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic...

    Authors: Guilherme Henrique Gebim Polizel, Wellison J. S. Diniz, Aline Silva Mello Cesar, German D. Ramírez-Zamudio, Angela Cánovas, Evandro Fernando Ferreira Dias, Arícia Christofaro Fernandes, Barbara Carolina Teixeira Prati, Édison Furlan, Gabriela do Vale Pombo and Miguel Henrique de Almeida Santana
    Citation: BMC Genomics 2025 26:359
    Content type: Research Published on:

  43. This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). A detailed comparis...

    Authors: Mostafa Rezapour, Aarthi Narayanan, Wyatt H. Mowery and Metin Nafi Gurcan
    Citation: BMC Genomics 2025 26:358
    Content type: Research Published on:

  44. The basic helix-loop-helix (bHLH) transcription factors are involved in the biosynthesis of various secondary metabolites. However, genome-wide studies on the bHLH gene family in ferns and their role in lignin bi...

    Authors: Xiong Huang, Jiangtao Fan, Cai Liu, Peiyun Wang, Hongfei Li, Gang Wang and Xiaohong Chen
    Citation: BMC Genomics 2025 26:357
    Content type: Research Published on:

  45. Rapid turnaround time for a third-field resolution deceased donor human leukocyte antigen (HLA) typing is critical to improve organ transplantation outcomes. Third generation DNA sequencing platforms such as O...

    Authors: Jalal Siddiqui, Rohita Sinha, James Grantham, Ronnie LaCombe, Judith R. Alonzo, Scott Cowden and Steven Kleiboeker
    Citation: BMC Genomics 2025 26:356
    Content type: Research Published on:

  46. The bacterium Myxococcus xanthus provides an important multicellular model for understanding stress responses. The regulatory proteins CsgA, FruA, and MrpC are essential to survive prolonged starvation by forming...

    Authors: Mark A. Farrugia, Ramya Rajagopalan and Lee Kroos
    Citation: BMC Genomics 2025 26:355
    Content type: Research Published on:

  47. Ethiopian mustard (Brassica carinata (A) Braun) is a promising oilseed crop with the potential for sustainable biofuel and bio-industrial applications. Despite the presence of diverse germplasms in Ethiopia, thei...

    Authors: Yirssaw Demeke Ambaw, Andargachew Gedebo Abitea and Temesgen Magule Olango
    Citation: BMC Genomics 2025 26:354
    Content type: Research Published on:

  48. Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-gene...

    Authors: Ke-Hui Feng, Yu-Hua Qi, Zhuang-Xin Ye, Ting Li, Gao-Yang Jiao, Chuan-Xi Zhang, Jian-Ping Chen, Gang Lu and Jun-Min Li
    Citation: BMC Genomics 2025 26:353
    Content type: Research Published on:

  49. The Yunshang Black Goat, a distinguished meat goat breed native to China, is renowned for its superior reproductive capabilities. Despite this, there is considerable phenotypic variability within the breed. Du...

    Authors: Xiaolong Du, Yufang Liu, Xiaoyun He, Lin Tao, Meiying Fang and Mingxing Chu
    Citation: BMC Genomics 2025 26:349
    Content type: Research Published on:

  50. The CYP450 family members have been extensively studied in plants, where they play essential roles in metabolism, responses to biotic and abiotic stresses, and the regulation of growth and development. However...

    Authors: Xun Liu, Xinmin Liang, Jing Han, Yuqin Cui, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng and Xiaolan He
    Citation: BMC Genomics 2025 26:346
    Content type: Research Published on:

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BMC Genomics

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