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  1. Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example,...

    Authors: Benjamin D. Young, Olivia M. Williamson, Nicholas S. Kron, Natalia Andrade Rodriguez, Lys M. Isma, Nicholas J. MacKnight, Erinn M. Muller, Stephanie M. Rosales, Stephanie M. Sirotzke, Nikki Traylor-Knowles, Sara D. Williams and Michael S. Studivan
    Citation: BMC Genomics 2024 25:226
  2. In epigenetic modification, histone modification and DNA methylation coordinate the regulation of spermatogonium. Not only can methylcytosine dioxygenase 1 (TET1) function as a DNA demethylase, converting 5-me...

    Authors: Jin Wang, Lingling Liu, Zebin Li, Haoyu Wang, Yuanyuan Ren, Kaisheng Wang, Yang Liu, Xinjie Tao and Liming Zheng
    Citation: BMC Genomics 2024 25:225
  3. Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stre...

    Authors: Vasudevan Ayyappan, Venkateswara R. Sripathi, Shaojun Xie, Malay C. Saha, Rita Hayford, Desalegn D. Serba, Mayavan Subramani, Jyothi Thimmapuram, Antonette Todd and Venu Kal Kalavacharla
    Citation: BMC Genomics 2024 25:223
  4. Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflo...

    Authors: Jianxiu Liu, Danjuan Zeng, Yang Huang, Lisha Zhong, Jialin Liao, Yuxing Shi, Haidu Jiang, Yajin Luo, Yu Liang and Shengfeng Chai
    Citation: BMC Genomics 2024 25:222
  5. Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are components of the wheat streak mosaic virus disease complex in the Great Plains region of the U.S.A. and elsewhere. Co-infection of wheat ...

    Authors: Inanc Soylu, Dilip K. Lakshman, Satyanarayana Tatineni, Leny C. Galvez and Amitava Mitra
    Citation: BMC Genomics 2024 25:221
  6. The appropriate mineral nutrients are essential for sheep growth and reproduction. However, traditional grazing sheep often experience mineral nutrient deficiencies, especially copper (Cu), due to inadequate m...

    Authors: Xiwei Jin, Lingbo Meng, Zhi Qi and Lan Mi
    Citation: BMC Genomics 2024 25:220
  7. Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality.

    Authors: Jinmei Zhu, Yongli Wang, Yongchun Su, Maiqing Zheng, Huanxian Cui and Zhiwu Chen
    Citation: BMC Genomics 2024 25:219
  8. The majority of CAKUT-associated CNVs overlap at least one miRNA gene, thus affecting the cellular levels of the corresponding miRNA. We aimed to investigate the potency of restitution of CNV-affected miRNA le...

    Authors: Kristina Mitrovic, Ivan Zivotic, Ivana Kolic, Jelena Zakula, Maja Zivkovic, Aleksandra Stankovic and Ivan Jovanovic
    Citation: BMC Genomics 2024 25:218
  9. The genomic region that lies between the telomere and chromosome body, termed the subtelomere, is heterochromatic, repeat-rich, and frequently undergoes rearrangement. Within this region, large-scale structura...

    Authors: T Brann, A Beltramini, C Chaparro, M Berriman, SR Doyle and AV Protasio
    Citation: BMC Genomics 2024 25:217
  10. Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenens...

    Authors: Haichen Wang, Fengjun Xia, Yubing Xia, Jun Li, Yongmei Hu, Yating Deng and Mingxiang Zou
    Citation: BMC Genomics 2024 25:216
  11. Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fis...

    Authors: Marcela Alvarenga, Ananda Krishna Pereira D’Elia, Graciane Rocha, Clara Alvarez Arantes, Frederico Henning, Ana Tereza Ribeiro de Vasconcelos and Antonio Mateo Solé-Cava
    Citation: BMC Genomics 2024 25:215
  12. Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica).

    Authors: Pengxiang Zhu, Haiyan Li, Tailiang Lu, Ruizheng Liang and Baoxiong Wan
    Citation: BMC Genomics 2024 25:214
  13. The stria vascularis (SV), located in the lateral wall of the cochlea, maintains cochlear fluid homeostasis and mechanoelectrical transduction (MET) activity required for sound wave conduction. The pathogenesi...

    Authors: Xi Gu, Kanglun Jiang, Ruru Chen, Zhifeng Chen, Xianmin Wu, Haijie Xiang, Xinsheng Huang and Benyu Nan
    Citation: BMC Genomics 2024 25:213
  14. Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. Howe...

    Authors: Tao Zhou, Yadi Tang, Lipan Zhou, Jie Liu, Yang Pu, Fan Jiang, Jian Wang and Xumei Wang
    Citation: BMC Genomics 2024 25:212
  15. Due to its enormous biomass, Antarctic krill (Euphausia superba) plays a crucial role in the Antarctic Ocean ecosystem. In recent years, Antarctic krill has found extensive application in aquaculture, emerging as...

    Authors: Mengya Wang, Shaoxuan Wu, Hui Ding, Mingyi Wang, Jiayi Ma, Jie Xiao, Bo Wang, Zhenmin Bao and Jingjie Hu
    Citation: BMC Genomics 2024 25:210
  16. The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild ...

    Authors: Jia Liu, Luyang Wei, Yirong Wu, Zongkuan Wang, Haiyan Wang, Jin Xiao, Xiue Wang and Li Sun
    Citation: BMC Genomics 2024 25:209
  17. Polycystic ovary syndrome (PCOS) is a complex multifactorial disorder with a substantial genetic component. However, the clinical manifestations of PCOS are heterogeneous with notable differences between lean ...

    Authors: Kharis Burns, Benjamin H. Mullin, Loes M. E. Moolhuijsen, Triin Laisk, Jaakko S. Tyrmi, Jinrui Cui, Ky’Era V. Actkins, Yvonne V. Louwers, Lea K. Davis, Frank Dudbridge, Ricardo Azziz, Mark O. Goodarzi, Hannele Laivuori, Reedik Mägi, Jenny A. Visser, Joop S. E. Laven…
    Citation: BMC Genomics 2024 25:208
  18. Darjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor seed germination, and viability, as well as issues with vegetative prop...

    Authors: Vivek Kumar Awon, Debabrata Dutta, Saptadipa Banerjee, Soumili Pal and Gaurab Gangopadhyay
    Citation: BMC Genomics 2024 25:207
  19. Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a five-year survival rate of approximately 10%. Genetic mutations are pivotal drivers in PDAC pathogenesis, but recent investigations also re...

    Authors: Wenrui Han, Detong Shi, Qiu Yang, Xinxin Li, Jian Zhang, Cheng Peng and Fang Yan
    Citation: BMC Genomics 2024 25:206
  20. Immunogenic cell death (ICD) has been identified as regulated cell death, which is sufficient to activate the adaptive immune response. This study aimed to research ICD-related genes and create a gene model to...

    Authors: Xiaobo Wang, Tianxiang Ren, Chuting Liao, Yong Xie and Jing Cao
    Citation: BMC Genomics 2024 25:205
  21. Medicago truncatula, model legume and alfalfa relative, has served as an essential resource for advancing our understanding of legume physiology, functional genetics, and crop improvement traits. Necrotrophic fun...

    Authors: Jacob R. Botkin, Andrew D. Farmer, Nevin D. Young and Shaun J. Curtin
    Citation: BMC Genomics 2024 25:204
  22. Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat pr...

    Authors: Ya-li Li, Li-yun Nie, Shuang-wen Deng, Lei Duan, Zheng-feng Wang, Joseph L.M. Charboneau, Boon-Chuan Ho and Hong-feng Chen
    Citation: BMC Genomics 2024 25:203
  23. Transitions from sexual to asexual reproduction are common in eukaryotes, but the underlying mechanisms remain poorly known. The pea aphid—Acyrthosiphon pisum—exhibits reproductive polymorphism, with cyclical par...

    Authors: M. D. Huguet, S. Robin, S. Hudaverdian, S. Tanguy, N. Leterme-Prunier, R. Cloteau, S. Baulande, P. Legoix-Né, F. Legeai, J.-C. Simon, J. Jaquiéry, D. Tagu and G. Le Trionnaire
    Citation: BMC Genomics 2024 25:202
  24. To gain a deeper understanding of the metabolic differences within and outside the body, as well as changes in transcription levels following estrus in yaks, we conducted transcriptome and metabolome analyses ...

    Authors: Huangqing Zhao, Yongzhen Huang, Shi Shu, Guowen Wang, Changqi Fu, Rong Huang, Jun Zhang, Huawei Su, Yang He, Chuzhao Lei, Lei Du, Jiahao Zhao and Wei Peng
    Citation: BMC Genomics 2024 25:201
  25. Calmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has bee...

    Authors: Dong Yang, Ting Chen, Yushuang Wu, Huiquan Tang, Junyi Yu, Xiaoqiu Dai, Yixiong Zheng, Xiaorong Wan, Yong Yang and Xiaodan Tan
    Citation: BMC Genomics 2024 25:200
  26. Abiotic stresses in plants include all the environmental conditions that significantly reduce yields, like drought and heat. One of the most significant effects they exert at the cellular level is the accumula...

    Authors: Marco Moroldo, Nicolas Blanchet, Harold Duruflé, Stéphane Bernillon, Thierry Berton, Olivier Fernandez, Yves Gibon, Annick Moing and Nicolas B. Langlade
    Citation: BMC Genomics 2024 25:199
  27. Cervical cancer (CC) causes more than 311,000 deaths annually worldwide. The integration of human papillomavirus (HPV) is a crucial genetic event that contributes to cervical carcinogenesis. Despite HPV DNA in...

    Authors: Zhijie Wang, Chen Liu, Wanxin Liu, Xinyi Lv, Ting Hu, Fan Yang, Wenhui Yang, Liang He and Xiaoyuan Huang
    Citation: BMC Genomics 2024 25:198
  28. In cold and temperate zones, seasonal reproduction plays a crucial role in the survival and reproductive success of species. The photoperiod influences reproductive processes in seasonal breeders through the h...

    Authors: Jianye Chang, Yanglong Xu, Yuting Fu, Jiaxin Liu, Danli Jiang, Jianqiu Pan, Hongjia Ouyang, Wenjun Liu, Jin Xu, Yunbo Tian, Yunmao Huang, Jue Ruan and Xu Shen
    Citation: BMC Genomics 2024 25:197
  29. Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in ot...

    Authors: Priya Yadav, Ankeet Kumar, Sujith S Nath, Yashas Devasurmutt, Geetha Shashidhar, Madhvi Joshi, Apurvasinh Puvar, Sonal Sharma, Janvi Raval, Rameshchandra Pandit, Priyank Chavda, Sudeep Nagaraj, Yogisharadhya Revanaiah, Deepak Patil, S K Raval, Jigar Raval…
    Citation: BMC Genomics 2024 25:196
  30. Lipoxygenase (LOX) is a multifunctional enzyme that is primarily related to plant organ growth and development, biotic and abiotic stress responses, and production of flavor-associated metabolites. In higher p...

    Authors: Lei Xu, Xiaoxi Zhu, Fengyan Yi, Yajiao Liu, Bilig Sod, Mingna Li, Lin Chen, Junmei Kang, Qingchuan Yang and Ruicai Long
    Citation: BMC Genomics 2024 25:195
  31. Bone morphogenetic proteins (BMPs) are part of the transforming growth factor beta (TGF-β) superfamily and play crucial roles in bone development, as well as in the formation and maintenance of various organs. Tr...

    Authors: Yizheng Zhang, Jinhui Yu, Rui Han, Zhigang Ma, Meng Zhang, Yikai Li, Yongtao Tang, Guoxing Nie and Chuanjiang Zhou
    Citation: BMC Genomics 2024 25:194
  32. The application of biotechnologies which make use of genetic markers in chicken breeding is developing rapidly. Diversity Array Technology (DArT) is one of the current Genotyping-By-Sequencing techniques allow...

    Authors: Valentin Mujyambere, Kwaku Adomako and Oscar Simon Olympio
    Citation: BMC Genomics 2024 25:193
  33. Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, th...

    Authors: Tom Pennance, Javier Calvelo, Jacob A. Tennessen, Ryan Burd, Jared Cayton, Stephanie R. Bollmann, Michael S. Blouin, Johannie M. Spaan, Federico G. Hoffmann, George Ogara, Fredrick Rawago, Kennedy Andiego, Boaz Mulonga, Meredith Odhiambo, Eric S. Loker, Martina R. Laidemitt…
    Citation: BMC Genomics 2024 25:192
  34. Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is one of the devastating diseases in crop production, seriously reducing the yield of crops. R. pseudosolanacearum, is known for its broad i...

    Authors: Shanwen Ding, Zijun Ma, Lin Yu, Guobing Lan, Yafei Tang, Zhenggang Li, Zifu He and Xiaoman She
    Citation: BMC Genomics 2024 25:191
  35. Non-alcoholic fatty liver disease (NAFLD) has rapidly become the most common cause of chronic liver disease in children and adolescents, but its etiology remains largely unknown. Adrenarche is a critical phase...

    Authors: Haoqing Li, Yingyu Liu, Fengyan Meng, Junan Chen and Xingfa Han
    Citation: BMC Genomics 2024 25:190
  36. CRISPR-Cas9 technology has advanced in vivo gene therapy for disorders like hemophilia A, notably through the successful targeted incorporation of the F8 gene into the Alb locus in hepatocytes, effectively cur...

    Authors: Juan-Juan Zhao, Xin-Yu Sun, Sai-Ning Tian, Zong-Ze Zhao, Meng-Di Yin, Mei Zhao, Feng Zhang, Si-Ang Li, Zhi-Xue Yang, Wei Wen, Tao Cheng, An Gong, Jian-Ping Zhang and Xiao-Bing Zhang
    Citation: BMC Genomics 2024 25:189
  37. Haemonchus contortus (H. contortus) is the most common parasitic nematode in ruminants and is prevalent worldwide. H. contortus resistance to albendazole (ABZ) hinders the efficacy of anthelmintic drugs, but litt...

    Authors: Xindi Chen, Tengyu Wang, Wenrui Guo, Xu Yan, Huilin Kou, Yu Yu, Chunxia Liu, Wa Gao, Wenlong Wang and Rui Wang
    Citation: BMC Genomics 2024 25:188
  38. Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routine...

    Authors: Katerina Kvapilova, Pavol Misenko, Jan Radvanszky, Ondrej Brzon, Jaroslav Budis, Juraj Gazdarica, Ondrej Pos, Marie Korabecna, Martin Kasny, Tomas Szemes, Petr Kvapil, Jan Paces and Zbynek Kozmik
    Citation: BMC Genomics 2024 25:187
  39. Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom...

    Authors: Cassandra M. Modahl, Summer Xia Han, Jory van Thiel, Candida Vaz, Nathan L. Dunstan, Seth Frietze, Timothy N. W. Jackson, Stephen P. Mackessy and R. Manjunatha Kini
    Citation: BMC Genomics 2024 25:186
  40. Alpaca is a domestic South American camelid probably arising from the domestication of two wild camelids, the vicugna and the guanaco. Two phenotypes are described for alpaca, known as huacaya and suri. Huacay...

    Authors: Stefano Pallotti, Matteo Picciolini, Giovanni Deiana, Dario Pediconi, Marco Antonini, Valerio Napolioni and Carlo Renieri
    Citation: BMC Genomics 2024 25:185
  41. Almost all extant organisms use the same, so-called canonical, genetic code with departures from it being very rare. Even more exceptional are the instances when a eukaryote with non-canonical code can be easi...

    Authors: Fred R. Opperdoes, Kristína Záhonová, Ingrid Škodová-Sveráková, Barbora Bučková, Ľubomíra Chmelová, Julius Lukeš and Vyacheslav Yurchenko
    Citation: BMC Genomics 2024 25:184
  42. Ovarian cancer (OC) has the worst prognosis among gynecological malignancies, most of which are found to be in advanced stage. Cell reduction surgery based on platinum-based chemotherapy is the current standar...

    Authors: Wei Li, Limei Huang, Nana Qi, Qinle Zhang and Zailong Qin
    Citation: BMC Genomics 2024 25:183
  43. Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried ou...

    Authors: Yujiao Wang, Hongjuan Wang, Chun Yu, Xiaoming Yan, Jiasong Chu, Benli Jiang and Jiabao Zhu
    Citation: BMC Genomics 2024 25:182
  44. Next-generation Sequencing (NGS) combined with bioinformatic analyses constitutes a powerful approach for identifying and characterizing previously unknown viral genomes. In this study, leaf samples from bitte...

    Authors: Shahrbanou Ghorani, Hossein Massumi, Samin H. Farhangi, Mehdi Mansouri, Jahangir Heydarnejad and Akbar Hosseinipour
    Citation: BMC Genomics 2024 25:181
  45. Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management p...

    Authors: Jordan Brungardt, Yanina Alarcon, Jason Shiller, Carolyn Young, Maria J. Monteros, Jennifer J. Randall and Clive H. Bock
    Citation: BMC Genomics 2024 25:180
  46. Acute Hepatopancreatic Necrosis Disease (AHPND) causes significant mortality in shrimp aquaculture. The infection is primarily instigated by Vibrio parahaemolyticus (Vp) strains carrying a plasmid encoding the bi...

    Authors: Marieke Vandeputte, Sieglinde Coppens, Peter Bossier, Nick Vereecke and Daisy Vanrompay
    Citation: BMC Genomics 2024 25:178
  47. Prion diseases, also known as transmissible spongiform encephalopathies (TSEs) remain one of the deleterious disorders, which have affected several animal species. Polymorphism of the prion protein (PRNP) gene ma...

    Authors: Adeniyi C. Adeola, Semiu F. Bello, Abdussamad M. Abdussamad, Rahamon A. M. Adedokun, Sunday C. Olaogun, Nasiru Abdullahi, Akanbi I. Mark, Anyebe B. Onoja, Oscar J. Sanke, Godwin F. Mangbon, Jebi Ibrahim, Philip M. Dawuda, Adebowale E. Salako, Samia Kdidi and Mohamed Habib Yahyaoui
    Citation: BMC Genomics 2024 25:177
  48. Brain diseases pose a significant threat to human health, and various network-based methods have been proposed for identifying gene biomarkers associated with these diseases. However, the brain is a complex sy...

    Authors: Ping Zhang, Weihan Zhang, Weicheng Sun, Jinsheng Xu, Hua Hu, Lei Wang and Leon Wong
    Citation: BMC Genomics 2024 25:175

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