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  1. Downy mildew disease of sunflower, caused by the obligate biotrophic oomycete Plasmopara halstedii, can have significant economic impact on sunflower cultivation. Using high-throughput whole transcriptome sequenc...

    Authors: Sakshi Bharti, Sebastian Ploch and Marco Thines
    Citation: BMC Genomics 2023 24:140
  2. Non-human primates, such as Rhesus macaques, are a powerful model for studies of the cellular and physiological effects of radiation, development of radiation biodosimetry, and for understanding the impact of ...

    Authors: Shanaz A. Ghandhi, Shad R. Morton, Igor Shuryak, Younghyun Lee, Rajesh K. Soni, Jay R. Perrier, James Bakke, Janet Gahagan, Kim Bujold, Simon Authier, Sally A. Amundson, David J. Brenner, Denise Nishita, Polly Chang and Helen C. Turner
    Citation: BMC Genomics 2023 24:139
  3. Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree. Its fruit quality and yield are affected by embryo development. As a plant seed germination marker gene, the germin-like prote...

    Authors: Zhuoyun Li, Zhuoran Fu, Shuting Zhang, Xueying Zhang, Xiaodong Xue, Yukun Chen, Zihao Zhang, Zhongxiong Lai and Yuling Lin
    Citation: BMC Genomics 2023 24:138
  4. Background: Autozygosity, the proportion of the genome that is homozygous by descent, has been associated with variation in multiple health-related traits impacting evolutionary fitness. Autozygosity (FROH) is ty...

    Authors: Megan T. Lynch, Kristin A. Maloney, Huichun Xu, James A. Perry, Regeneron Genetics Center, Alan R. Shuldiner and Braxton D. Mitchell
    Citation: BMC Genomics 2023 24:134
  5. Green feed diet in ruminants exerts a beneficial effect on rumen metabolism and enhances the content of milk nutraceutical quality. At present, a comprehensive analysis focused on the identification of genes, ...

    Authors: Angela Salzano, Salvatore Fioriniello, Nunzia D’Onofrio, Maria Luisa Balestrieri, Riccardo Aiese Cigliano, Gianluca Neglia, Floriana Della Ragione and Giuseppe Campanile
    Citation: BMC Genomics 2023 24:133
  6. Vascular endothelial growth factor A (VEGFA) is a major angiogenic factor that plays an important role in the formation of blood vessels during embryonic development. VEGFA has been implicated in the pathophys...

    Authors: Sheila Nabweyambo, Stephen Kanyerezi, John H.-O. Petterson, Fred Ashaba Katabazi, Alfred Ssekagiri, Savannah Mwesigwa, Gerald Mboowa, Faith Nakazzi, Annette Keesiga, Moses Adroma, Freddie Bwanga, Naomi McGovern, Obondo James Sande and Annettee Nakimuli
    Citation: BMC Genomics 2023 24:132
  7. Copy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods to predict the pathogenicity of CNVs are required to realize the relat...

    Authors: Kangqi Lv, Dayang Chen, Dan Xiong, Huamei Tang, Tong Ou, Lijuan Kan and Xiuming Zhang
    Citation: BMC Genomics 2023 24:131
  8. Since 20 years of research, free fatty acids receptors (FFARs) have received considerable attention in mammals. To date, four FFARs (FFAR1, FFAR2, FFAR3 and FFAR4) are especially studied owing to their physiol...

    Authors: Jérôme Roy, Elodie Baranek and Lucie Marandel
    Citation: BMC Genomics 2023 24:130
  9. Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the d...

    Authors: Feng Cheng, Alice B. Dennis, Josephine Ijeoma Osuoha, Julia Canitz, Frank Kirschbaum and Ralph Tiedemann
    Citation: BMC Genomics 2023 24:129
  10. Kidney stone also known as urolithiasis or nephrolithiasis, is one of the oldest diseases known to medicine, however, the gene expression changes and related kidney injury remains unclear.

    Authors: Wang Zhu, Deng Qiong, Gu Yanli, Li Min, Zhang Ying, Hu Qiyi, Zhang Shenping, Wang Xisheng and Liang Hui
    Citation: BMC Genomics 2023 24:127
  11. Late embryogenesis abundant (LEA) proteins play an important role in dehydration process of seed maturation. The seeds of Panax notoginseng (Burkill) F. H. Chen are typically characterized with the recalcitrance ...

    Authors: Jin-Shan Jia, Na Ge, Qing-Yan Wang, Li-Ting Zhao, Cui Chen and Jun-Wen Chen
    Citation: BMC Genomics 2023 24:126
  12. MicroRNAs (miRNAs) play a critical role in regulating skin pigmentation. As a key economic trait, skin color directly affects the market value of rainbow trout (Oncorhynchus mykiss), however, the regulatory mecha...

    Authors: Shenji Wu, Lu Zhao, Jinqiang Huang, Yongjuan Li, Zhe Liu and Dongqiang Zhang
    Citation: BMC Genomics 2023 24:124
  13. The termite-fungus symbiosis is an ancient stable mutualism of two partners that reproduce and disperse independently. With the founding of each termite colony the symbiotic association must be re-established ...

    Authors: Sabine M. E. Vreeburg, Ben Auxier, Bas Jacobs, Peter M. Bourke, Joost van den Heuvel, Bas J. Zwaan and Duur K. Aanen
    Citation: BMC Genomics 2023 24:123
  14. Regeneration studies help to understand the strategies that replace a lost or damaged organ and provide insights into approaches followed in regenerative medicine and engineering. Amphibians regenerate their l...

    Authors: Cuckoo Mahapatra, Pranati Naik, Sumanta Kumar Swain and Pratyush Paradarsita Mohapatra
    Citation: BMC Genomics 2023 24:122
  15. HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drou...

    Authors: Xing Liu, Liangchen Su, Limei Li, Zhi Zhang, Xiaoyun Li, Qingjian Liang and Ling Li
    Citation: BMC Genomics 2023 24:119
  16. More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production e...

    Authors: Bashir Salim, Saeed Alasmari, Nouh Saad Mohamed, Mohamed-Khair A. Ahmed, Ryo Nakao and Olivier Hanotte
    Citation: BMC Genomics 2023 24:118
  17. Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges hav...

    Authors: Scott Hotaling, Edward R. Wilcox, Jacqueline Heckenhauer, Russell J. Stewart and Paul B. Frandsen
    Citation: BMC Genomics 2023 24:117
  18. Cross breeding is an important way to improve livestock performance. As an important livestock and poultry resource in Henan Province of China, Bohuai goat was formed by crossing Boer goat and Huai goat. After...

    Authors: Zhi Yao, Shunjin Zhang, Xianwei Wang, Yingwei Guo, Xiaoling Xin, Zijing Zhang, Zejun Xu, Eryao Wang, Yu Jiang and Yongzhen Huang
    Citation: BMC Genomics 2023 24:116
  19. Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is...

    Authors: Martyna Marynowska, David Sillam-Dussès, Boris Untereiner, Dominika Klimek, Xavier Goux, Piotr Gawron, Yves Roisin, Philippe Delfosse and Magdalena Calusinska
    Citation: BMC Genomics 2023 24:115
  20. Echinococcus granulosus sensu lato has a complex developmental biology with a variety of factors relating to both intermediate and final hosts. To achieve maximum parasite adaptability, the development of the ces...

    Authors: Mohammad Ali Mohammadi, Mehdi Mansouri, Ali Derakhshani, Masoud Rezaie, Mehdi Borhani, Saeid Nasibi, Seyed Mohammad Mousavi, Ali Afgar, Natalia Macchiaroli, Mara C. Rosenzvit and Majid Fasihi Harandi
    Citation: BMC Genomics 2023 24:114
  21. Chloroplast genomes for 3 Bidens plants endemic to China (Bidens bipinnata Linn., Bidens pilosa Linn., and Bidens alba var. radiata) have been sequenced, assembled and annotated in this study to distinguish their...

    Authors: Danchun Zhang, Jiajun Tu, Xiaoxia Ding, Wan Guan, Lu Gong, Xiaohui Qiu, Zhihai Huang and He Su
    Citation: BMC Genomics 2023 24:113
  22. The mass production of natural predators with prolonged shelf life is a prerequisite for their field application as pest control agents. The traditional methods used for the mass production of Serangium japonicum

    Authors: Shaukat Ali, Jing Peng, Jian-Feng Liang, Chuyang Huang, Yong-Hui Xie and Xingmin Wang
    Citation: BMC Genomics 2023 24:112
  23. The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and y...

    Authors: William A Marsh, Selina Brace and Ian Barnes
    Citation: BMC Genomics 2023 24:111
  24. Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand ...

    Authors: Ruiqi Zhang, Fusheng Yao, Xue Cheng, Mengyuan Yang and Zhonghua Ning
    Citation: BMC Genomics 2023 24:110
  25. Follicle selection in chickens refers to the process of selecting one follicle from a group of small yellow follicles (SY, 6–8 mm in diameter) for development into 12–15 mm hierarchal follicles (usually F6 fol...

    Authors: Yanhong Zhang, Qiuyue Chen, Yuanyuan Guo, Li Kang, Yi Sun and Yunliang Jiang
    Citation: BMC Genomics 2023 24:109
  26. The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to R...

    Authors: Yan Ren, Elizabeth Tseng, Timothy P. L. Smith, Stefan Hiendleder, John L. Williams and Wai Yee Low
    Citation: BMC Genomics 2023 24:108
  27. The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is near...

    Authors: Yen On Chan, Nicholas Dietz, Shuai Zeng, Juexin Wang, Sherry Flint-Garcia, M. Nancy Salazar-Vidal, Mária Škrabišová, Kristin Bilyeu and Trupti Joshi
    Citation: BMC Genomics 2023 24:107
  28. Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cell...

    Authors: Angela Pelusi, Luca Ambrosino, Marco Miralto, Maria Luisa Chiusano, Alessandra Rogato, Maria Immacolata Ferrante and Marina Montresor
    Citation: BMC Genomics 2023 24:106
  29. Xanthomonas campestris pv. campestris (Xcc) is an important seed-borne plant pathogenic bacteria that can cause a serious threat to cruciferous crops. Bacteria can enter into the viable but non-culturable (VBNC) ...

    Authors: Kaihong Bai, Xiaoli Xu, Xudong Wang, Yao Li, Chengxuan Yu, Na Jiang, Jianqiang Li and Laixin Luo
    Citation: BMC Genomics 2023 24:105
  30. Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to nitrogen metabolic genes using the PATRIC,...

    Authors: Preeti Thakur and Pammi Gauba
    Citation: BMC Genomics 2023 24:104
  31. Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color o...

    Authors: Daozong Chen, Haidong Chen, Guoqiang Dai, Haimei Zhang, Yi Liu, Wenjie Shen, Bo Zhu, Cheng Cui and Chen Tan
    Citation: BMC Genomics 2023 24:103
  32. The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive developme...

    Authors: Iamshchikov Pavel, Larionova Irina, Gerashchenko Tatiana, Piankov Denis, Koshkin Philipp, Korostelev Sergei and Denisov Evgeny
    Citation: BMC Genomics 2023 24:102
  33. Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors and approximately 5% of patients with chronic pancreatitis (CP) inevitably develop PDAC. This study aims explore the key gene regulat...

    Authors: Zhirong Zhao, Qiang Luo, Yi Liu, Kexin Jiang, Lichen Zhou, Ruiwu Dai and Han Wang
    Citation: BMC Genomics 2023 24:101
  34. Apis cerana is widely distributed in China and, prior to the introduction of western honeybees, was the only bee species kept in China. During the long-term natural evolutionary process, many unique phenotypic va...

    Authors: Yi Zhang, Hao Xu, Zhi Wang, Haoliang Jie, Fuchao Gao, Minqi Cai, Kang Wang, Dafu Chen, Rui Guo, Zheguang Lin, Qingsheng Niu and Ting Ji
    Citation: BMC Genomics 2023 24:100
  35. In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko

    Authors: Chunliu Pan, Lixiang Yao, Liying Yu, Zhu Qiao, Meiqiong Tang, Fan Wei, Xueyan Huang and Yunyi Zhou
    Citation: BMC Genomics 2023 24:99
  36. Serum biochemical indicators are often regarded as direct reflections of animal metabolism and health. The molecular mechanisms underlying serum biochemical indicators metabolism of chicken (Gallus Gallus) hav...

    Authors: Haijie Song, Wenting Li, Yuanfang Li, Bin Zhai, Yujie Guo, Yi Chen, Ruili Han, Guirong Sun, Ruirui Jiang, Zhuanjian Li, Fengbin Yan, Guoxi Li, Xiaojun Liu, Yanhua Zhang, Yadong Tian and Xiangtao Kang
    Citation: BMC Genomics 2023 24:98
  37. Long read’ sequencing methods have been used to identify previously uncharacterized structural variants that cause human genetic diseases. Therefore, we investigated whether long read sequencing could facilitate...

    Authors: Ahmed Arslan, Zhuoqing Fang, Meiyue Wang, Yalun Tan, Zhuanfen Cheng, Xinyu Chen, Yuan Guan, Laura J. Pisani, Boyoung Yoo, Gill Bejerano and Gary Peltz
    Citation: BMC Genomics 2023 24:97
  38. Serum microRNAs (miRNAs) are promising non-invasive biomarkers for diagnosing glioma. However, most reported predictive models are constructed without a large enough sample size, and quantitative expression le...

    Authors: Hongdong Li, Liyuan Ma, Fengyuan Luo, Wenkai Liu, Na Li, Tao Hu, Haijian Zhong, You Guo and Guini Hong
    Citation: BMC Genomics 2023 24:96
  39. Acanthocephala is a clade of obligate endoparasites whose mitochondrial genomes (mitogenomes) and evolution remain relatively poorly understood. Previous studies reported that atp8 is lacking from acanthocephalan...

    Authors: Jin-Wei Gao, Xi-Ping Yuan, Ivan Jakovlić, Hao Wu, Chuan-Yu Xiang, Min Xie, Rui Song, Zhong-Gui Xie, Yuan-An Wu and Dong-Sheng Ou
    Citation: BMC Genomics 2023 24:95
  40. Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Cop...

    Authors: Hee Ju Hwang, Bharat Bhusan Patnaik, Snigdha Baliarsingh, Hongray Howrelia Patnaik, Min Kyu Sang, Jie eun Park, Hang Chul Cho, Dae Kwon Song, Jun Yang Jeong, Chan Eui Hong, Yong Tae Kim, Hyeon Jun Sin, Liu Ziwei, So Young Park, Se Won Kang, Heon Cheon Jeong…
    Citation: BMC Genomics 2023 24:94
  41. The quorum-sensing molecule farnesol, in opportunistic yeast Candida albicans, modulates its dimorphic switch between yeast and hyphal forms, and biofilm formation. Although there is an increasing interest in far...

    Authors: Sima Mohammadi, Annie Leduc, Steve J. Charette, Jean Barbeau and Antony T. Vincent
    Citation: BMC Genomics 2023 24:93
  42. Non-alcoholic fatty liver disease (NAFLD) is one of most common diseases in the world. Recently, alternative splicing (AS) has been reported to play a key role in NAFLD processes in mammals. Ducks can quickly ...

    Authors: Yiming Wang, Linfei Song, Mengfei Ning, Jiaxiang Hu, Han Cai, Weitao Song, Daoqing Gong, Long Liu, Jacqueline Smith, Huifang Li and Yinhua Huang
    Citation: BMC Genomics 2023 24:92
  43. The high similarity in anatomical and neurophysiological processes between pigs and humans make pigs an excellent model for metabolic diseases and neurological disorders. Lipids are essential for brain structu...

    Authors: Bruna Pereira da Silva, Simara Larissa Fanalli, Julia Dezen Gomes, Vivian Vezzoni de Almeida, Heidge Fukumasu, Felipe André Oliveira Freitas, Gabriel Costa Monteiro Moreira, Bárbara Silva-Vignato, James Mark Reecy, James Eugene Koltes, Dawn Koltes, Júlio Cesar de Carvalho Balieiro, Severino Matias de Alencar, Julia Pereira Martins da Silva, Luiz Lehmann Coutinho, Juliana Afonso…
    Citation: BMC Genomics 2023 24:91
  44. Aconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum spe...

    Authors: Niu Yanfei, Su Tai, Wu Chunhua, Deng Jia and Yang Fazhong
    Citation: BMC Genomics 2023 24:90

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