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  1. Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in Populus deltoids has not ye...

    Authors: Xiao-jing Wang, Xu-qian Peng, Xiao-chun Shu, Yu-hang Li, Zhong Wang and Wei-bing Zhuang
    Citation: BMC Genomics 2022 23:244
    Content type: Research Published on:

  2. External environmental factors, such as salt, alkali and drought, severely limit the acreage and yield of alfalfa. The mining of tolerance-related genes in alfalfa and improving the stress resistance of this p...

    Authors: Yuying Yuan, Jinqiu Yu, Lingzelai Kong, Wenkai Zhang, Xiangyin Hou and Guowen Cui
    Citation: BMC Genomics 2022 23:243
    Content type: Research Published on:

  3. An important aspect of studying evolution is to understand how new species are formed and their uniqueness is maintained. Hybridization can lead to the formation of new species through reorganization of the ad...

    Authors: Qianhong Gu, Shi Wang, Hui Zhong, Hui Yuan, Junliu Yang, Conghui Yang, Xuexue Huang, Xiaowei Xu, Yude Wang, Zehong Wei, Jing Wang and Shaojun Liu
    Citation: BMC Genomics 2022 23:242
    Content type: Research Published on:

  5. The emerging epitranscriptome plays an essential role in female fertility. As the most prevalent internal mRNA modification, N6-methyladenine (m6A) methylation regulate mRNA fate and translational efficiency. How...

    Authors: Chang Liu, Linshuang Li, Bo Yang, Yiqing Zhao, Xiyuan Dong, Lixia Zhu, Xinling Ren, Bo Huang, Jing Yue, Lei Jin, Hanwang Zhang and Lan Wang
    Citation: BMC Genomics 2022 23:240
    Content type: Research Published on:

  6. Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide....

    Authors: Ping Xu, Hui Li, Xiaohua Wang, Ge Zhao, Xiaofei Lu, Shengjie Dai, Xiaoyu Cui, Mei Yuan and Zhenning Liu
    Citation: BMC Genomics 2022 23:239
    Content type: Research Published on:

  7. Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure pres...

    Authors: Qiutao Ding, Runsheng Li, Xiaoliang Ren, Lu-yan Chan, Vincy W. S. Ho, Dongying Xie, Pohao Ye and Zhongying Zhao
    Citation: BMC Genomics 2022 23:238
    Content type: Research article Published on:

  9. Skin pigmentation is a broadly appearing phenomenon of most animals and humans in nature. Here we used a bird model to investigate why melanin spot deposits on the skin.

    Authors: Hehe Liu, Jianmei Wang, Jian Hu, Lei Wang, Zhanbao Guo, Wenlei Fan, Yaxi Xu, Dapeng Liu, Yunsheng Zhang, Ming Xie, Jing Tang, Wei Huang, Qi Zhang, Zhengkui Zhou and Shuisheng Hou
    Citation: BMC Genomics 2022 23:236
    Content type: Research Published on:

  10. Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinfor...

    Authors: Federica Palma, Iolanda Mangone, Anna Janowicz, Alexandra Moura, Alexandra Chiaverini, Marina Torresi, Giuliano Garofolo, Alexis Criscuolo, Sylvain Brisse, Adriano Di Pasquale, Cesare Cammà and Nicolas Radomski
    Citation: BMC Genomics 2022 23:235
    Content type: Research Published on:

  12. Abscisic acid (ABA) is a phytohormone that plays important roles in the regulation of plant growth, seed germination, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein, an ABA receptor, ...

    Authors: Guoming Wang, Kaijie Qi, Xin Gao, Lei Guo, Peng Cao, Qionghou Li, Xin Qiao, Chao Gu and Shaoling Zhang
    Citation: BMC Genomics 2022 23:233
    Content type: Research Published on:

  13. The application of RNA-seq technology has become more extensive and the number of analysis procedures available has increased over the past years. Selecting an appropriate workflow has become an important issu...

    Authors: Xu Liu, Jialu Zhao, Liting Xue, Tian Zhao, Wei Ding, Yuying Han and Haihong Ye
    Citation: BMC Genomics 2022 23:232
    Content type: Research Published on:

  14. The cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance.

    Authors: Chaochen Huang, Pengbo Li, Junfeng Cao, Zishou Zheng, Jinquan Huang, Xiufang Zhang, Xiaoxia Shangguan, Lingjian Wang and Zhiwen Chen
    Citation: BMC Genomics 2022 23:231
    Content type: Research Published on:

  16. The soil-dwelling nematode Caenorhabditis elegans serves as a model system to study innate immunity against microbial pathogens. C. elegans have been collected from around the world, where they, presumably, adapt...

    Authors: Patrick Lansdon, Maci Carlson and Brian D. Ackley
    Citation: BMC Genomics 2022 23:229
    Content type: Research Published on:

  17. The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseas...

    Authors: David Konkin, Ya-Chih Hsueh, Morgan Kirzinger, Marie Kubaláková, Aparna Haldar, Margaret Balcerzak, Fangpu Han, George Fedak, Jaroslav Doležel, Andrew Sharpe and Thérèse Ouellet
    Citation: BMC Genomics 2022 23:228
    Content type: Research Published on:

  18. Genetic variants have been found to influence red blood cell (RBC) susceptibility to hemolytic stress and affect transfusion outcomes and the severity of blood diseases. Males have a higher susceptibility to h...

    Authors: Fang Fang, Kelsey Hazegh, Alan E. Mast, Darrell J. Triulzi, Bryan R. Spencer, Mark T. Gladwin, Michael P. Busch, Tamir Kanias and Grier P. Page
    Citation: BMC Genomics 2022 23:227
    Content type: Research Published on:

  19. BEC-producing Clostridium perfringens is a causative agent of foodborne gastroenteritis. It was first reported in 2014, and since then, several isolates have been identified in Japan and the United Kingdom. The n...

    Authors: Kengo Ueda, Kazuki Kawahara, Narumi Kimoto, Yusuke Yamaguchi, Kazuhiro Yamada, Hiroya Oki, Takuya Yoshida, Shigeaki Matsuda, Yuki Matsumoto, Daisuke Motooka, Kentaro Kawatsu, Tetsuya Iida, Shota Nakamura, Tadayasu Ohkubo and Shinya Yonogi
    Citation: BMC Genomics 2022 23:226
    Content type: Research Published on:

  20. The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of n...

    Authors: Jayanth Jawahar, Alexander W. McCumber, Colin R. Lickwar, Caroline R. Amoroso, Sol Gomez de la Torre Canny, Sandi Wong, Margaret Morash, James H. Thierer, Steven A. Farber, Brendan J. M. Bohannan, Karen Guillemin and John F. Rawls
    Citation: BMC Genomics 2022 23:225
    Content type: Research Published on:

  21. Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved ...

    Authors: Hojjat Asadollahpour Nanaei, Hamed Kharrati-Koopaee and Ali Esmailizadeh
    Citation: BMC Genomics 2022 23:224
    Content type: Research Published on:

  23. Mastitis is a very common disease in the dairy industry that producers encounter daily. Transcriptomics, using RNA-Sequencing (RNA - Seq) technology, can be used to study the functional aspect of mastitis resi...

    Authors: V. Asselstine, J. F. Medrano and A. Cánovas
    Citation: BMC Genomics 2022 23:222
    Content type: Research Published on:

  24. Environmental exposures in utero which modify DNA methylation may have a long-lasting impact on health and disease in offspring. We aimed to identify and replicate previously published genomic loci where DNA meth...

    Authors: Loubna Akhabir, Randa Stringer, Dipika Desai, Piush J Mandhane, Meghan B Azad, Theo J Moraes, Padmaja Subbarao, Stuart E Turvey, Guillaume Paré and Sonia S. Anand
    Citation: BMC Genomics 2022 23:221
    Content type: Research article Published on:

  26. Adipose tissue is an important endocrine and energy-storage organ in organisms, and it plays a crucial role in the energy-metabolism balance. Previous studies have found that sex-linked dwarf (SLD) chickens ge...

    Authors: Minmin Yang, Bowen Hu, Donglei Sun, Changbin Zhao, Haohui Wei, Dajian Li, Zhiying Liao, Yongxia Zhao, Jinping Liang, Meiqing Shi, Qingbin Luo, Qinghua Nie, Xiquan Zhang, Dexiang Zhang and Hongmei Li
    Citation: BMC Genomics 2022 23:219
    Content type: Research article Published on:

  27. Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically...

    Authors: Bicong Li, Tao Liu, Asjad Ali, Yao Xiao, Nan Shan, Jingyu Sun, Yingjin Huang, Qinghong Zhou and Qianglong Zhu
    Citation: BMC Genomics 2022 23:218
    Content type: Research Published on:

  28. Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirme...

    Authors: Emeline Cherchame, Laurent Guillier, Renaud Lailler, Marie-Leone Vignaud, Nathalie Jourdan-Da Silva, Simon Le Hello, François-Xavier Weill and Sabrina Cadel-Six
    Citation: BMC Genomics 2022 23:217
    Content type: Research Published on:

  30. Copy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, CNV is not well studied on the single-cell level except for humans and a few model organisms.

    Authors: Liu Yang, Yahui Gao, Adam Oswalt, Lingzhao Fang, Clarissa Boschiero, Mahesh Neupane, Charles G. Sattler, Cong-jun Li, Eyal Seroussi, Lingyang Xu, Lv Yang, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Yang Zhou…
    Citation: BMC Genomics 2022 23:215
    Content type: Research Published on:

  31. The “Assay for Transposase Accessible Chromatin sequencing” (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that has been widely used in multiple applications study...

    Authors: Hao Zhang, Michael E. Rice, Joseph W. Alvin, Dominique Farrera-Gaffney, James J. Galligan, Michael D. L. Johnson and Darren A. Cusanovich
    Citation: BMC Genomics 2022 23:214
    Content type: Research Published on:

  32. Recent evidences have suggested that human microorganisms participate in important biological activities in the human body. The dysfunction of host-microbiota interactions could lead to complex human disorders...

    Authors: Yu-An Huang, Zhi-An Huang, Jian-Qiang Li, Zhu-Hong You, Lei Wang, Hai-Cheng Yi and Chang-Qing Yu
    Citation: BMC Genomics 2022 22(Suppl 1):916
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 1

  33. Respectively, prostate cancer (PCa) and breast cancer (BC) are the second most and most commonly diagnosed cancer in men and women, and they account for a majority of cancer-related deaths world-wide. Cancer c...

    Authors: Yindan Lin, Ze Yang, Jingjia Li, Yandi Sun, Xueyun Zhang, Zihao Qu, Yan Luo and Lihong Zhang
    Citation: BMC Genomics 2022 23:213
    Content type: Research Published on:

  34. PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C2

    Authors: Elena Damm, Kristian K. Ullrich, William B. Amos and Linda Odenthal-Hesse
    Citation: BMC Genomics 2022 23:212
    Content type: Research Published on:

  36. Streptococcus thermophilus is a Gram-positive bacterium widely used as starter in the dairy industry as well as in many traditional fermented products. In addition to its technological importance, it has also gai...

    Authors: Emeline Roux, Aurélie Nicolas, Florence Valence, Grégoire Siekaniec, Victoria Chuat, Jacques Nicolas, Yves Le Loir and Eric Guédon
    Citation: BMC Genomics 2022 23:210
    Content type: Research Published on:

  37. A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been...

    Authors: Henrique Alberto Mulim, Luiz F. Brito, Luís Fernando Batista Pinto, José Bento Sterman Ferraz, Lais Grigoletto, Marcio Ribeiro Silva and Victor Breno Pedrosa
    Citation: BMC Genomics 2022 23:209
    Content type: Research Published on:

  38. Frequent occurrence of extreme high temperature is a major threat to crop production. Increasing evidence demonstrates that long non-coding RNAs (lncRNAs) have important biological functions in the regulation ...

    Authors: Xiaolin Hu, Qiye Wei, Hongying Wu, Yuanxiang Huang, Xiaojian Peng, Guomin Han, Qing Ma and Yang Zhao
    Citation: BMC Genomics 2022 23:208
    Content type: Research Published on:

  40. Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea

    Authors: Yulin Bai, Mei Wang, Ji Zhao, Huaqiang Bai, Xinyi Zhang, Jiaying Wang, Qiaozhen Ke, Ang Qu, Fei Pu, Weiqiang Zheng, Tao Zhou and Peng Xu
    Citation: BMC Genomics 2022 23:206
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:370

  41. Chilling injury of mung bean (Vigna radiata (L.)) during the blooming and podding stages is a major agricultural threat in Northeast China. Uniconazole (UNZ) can alleviate water deficit stress in soybean and wate...

    Authors: Hanqiao Hu, Naijie Feng, Xuefeng Shen, Liming Zhao and Dianfeng Zheng
    Citation: BMC Genomics 2022 23:205
    Content type: Research Published on:

  43. Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relati...

    Authors: Kewang Xu, Chenxue Lin, Shiou Yih Lee, Lingfeng Mao and Kaikai Meng
    Citation: BMC Genomics 2022 23:203
    Content type: Research Published on:

  44. Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encom...

    Authors: Arkadiy I. Garber, Catherine R. Armbruster, Stella E. Lee, Vaughn S. Cooper, Jennifer M. Bomberger and Sean M. McAllister
    Citation: BMC Genomics 2022 23:202
    Content type: Software Published on:

  45. Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs,...

    Authors: Erin M. Witkop, Dina A. Proestou and Marta Gomez-Chiarri
    Citation: BMC Genomics 2022 23:201
    Content type: Research Published on:

  46. Genomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in plant breeding. However, using predictors that are biologically closer...

    Authors: Po-Ya Wu, Benjamin Stich, Marius Weisweiler, Asis Shrestha, Alexander Erban, Philipp Westhoff and Delphine Van Inghelandt
    Citation: BMC Genomics 2022 23:200
    Content type: Research Published on:

  47. RAD51 proteins, which are conserved in all eukaryotes, repair DNA double-strand breaks. This is critical to homologous chromosome pairing and recombination enabling successful reproduction. Work in Arabidopsis...

    Authors: Claire Milsted, Bo Dai, Nelson Garcia, Lu Yin, Yan He, Shahryar Kianian, Wojciech Pawlowski and Changbin Chen
    Citation: BMC Genomics 2022 23:199
    Content type: Research Published on:

  48. Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest managem...

    Authors: Emma Bailey, Linda Field, Christopher Rawlings, Rob King, Fady Mohareb, Keywan-Hassani Pak, David Hughes, Martin Williamson, Eric Ganko, Benjamin Buer and Ralf Nauen
    Citation: BMC Genomics 2022 23:198
    Content type: Research Published on:

  49. Chemogenomic profiling is a powerful approach for understanding the genome-wide cellular response to small molecules. First developed in Saccharomyces cerevisiae, chemogenomic screens provide direct, unbiased ide...

    Authors: Marjan Barazandeh, Divya Kriti, Corey Nislow and Guri Giaever
    Citation: BMC Genomics 2022 23:197
    Content type: Research Published on:

  50. Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. Th...

    Authors: Jian-Rong Li, Mabel Tang, Yafang Li, Christopher I. Amos and Chao Cheng
    Citation: BMC Genomics 2022 23:196
    Content type: Research Published on:

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