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  1. Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human h...

    Authors: Dili Lai, Yue Fan, Guoxing Xue, Ailing He, Hao Yang, Chunlin He, Yijing Li, Jingjun Ruan, Jun Yan and Jianping Cheng
    Citation: BMC Genomics 2022 23:389
  2. Beef cuts in different regions of the carcass have different meat quality due to their distinct physiological function. The objective of this study was to characterize the region-specific expression difference...

    Authors: Tianliu Zhang, Tianzhen Wang, Qunhao Niu, Xu Zheng, Haipeng Li, Xue Gao, Yan Chen, Huijiang Gao, Lupei Zhang, George E. Liu, Junya Li and Lingyang Xu
    Citation: BMC Genomics 2022 23:387
  3. High yield and quality are essential goals of wheat (Triticum aestivum L.) breeding. Kernel length (KL), as a main component of kernel size, can indirectly change kernel weight and then affects yield. Identificat...

    Authors: Xinlin Xie, Shuiqin Li, Hang Liu, Qiang Xu, Huaping Tang, Yang Mu, Mei Deng, Qiantao Jiang, Guoyue Chen, Pengfei Qi, Wei Li, Zhien Pu, Ahsan Habib, Yuming Wei, Youliang Zheng, Xiujin Lan…
    Citation: BMC Genomics 2022 23:386
  4. As genomic sequencing moves closer to clinical implementation, there has been an increasing acceptance of returning incidental findings to research participants and patients for mutations in highly penetrant, ...

    Authors: Yen-Chen A. Feng, Ian B. Stanaway, John J. Connolly, Joshua C. Denny, Yuan Luo, Chunhua Weng, Wei-Qi Wei, Scott T. Weiss, Elizabeth W. Karlson and Jordan W. Smoller
    Citation: BMC Genomics 2022 23:385
  5. Cucumber is an important melon crop in the world, with different pericarp colors. However, the candidate genes and the underlying genetic mechanism for such an important trait in cucumber are unknown. In this ...

    Authors: Hongyu Huang, Qinqin Yang, Lidong Zhang, Weiliang Kong, Huizhe Wang, Aimin Wei, Shengli Du, Ruihuan Yang, Jiawang Li, Tao Lin, Xiaolin Geng and Yuhe Li
    Citation: BMC Genomics 2022 23:383
  6. Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecula...

    Authors: Qi Xiao, Youfu Lin, Hong Li, Yu Chen, Wei Wei, Peng Li and Lian Chen
    Citation: BMC Genomics 2022 23:382
  7. Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioin...

    Authors: Yan Zhu, Longxian Chen, Xiangna Hong, Han Shi and Xuan Li
    Citation: BMC Genomics 2022 23(Suppl 4):381

    This article is part of a Supplement: Volume 23 Supplement 4

  8. Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora...

    Authors: Ke Ma, Wei Chen, Shi-Qing Yan, Xiao-Qi Lin, Zhen-Zhen Liu, Jia-Bao Zhang, Yu Gao and Yong-Jun Yang
    Citation: BMC Genomics 2022 23:380
  9. Despite a multifactorial approach being taken for the evaluation of bull semen quality in many animal breeding centres worldwide, reliable prediction of bull fertility is still a challenge. Recently, attention...

    Authors: Miriama Štiavnická, Aurélie Chaulot-Talmon, Jean-Philippe Perrier, Petr Hošek, David A. Kenny, Patrick Lonergan, Hélène Kiefer and Sean Fair
    Citation: BMC Genomics 2022 23:379
  10. Oysters inhabit in the intertidal zone and may be suffered from environmental stresses, which can increase the production of reactive oxygen species (ROS), resulting in mass mortality. Superoxide dismutases (S...

    Authors: Youli Liu, Zhenmin Bao, Zhihua Lin and Qinggang Xue
    Citation: BMC Genomics 2022 23:378
  11. Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolv...

    Authors: Hong Zou, Fang-Lin Chen, Wen-Xiang Li, Ming Li, Hong-Peng Lei, Dong Zhang, Ivan Jakovlić and Gui-Tang Wang
    Citation: BMC Genomics 2022 23:376
  12. While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 ...

    Authors: Nisha Ghimire, Byeollee Kim, Chang-Muk Lee and Tae-Jin Oh
    Citation: BMC Genomics 2022 23:375
  13. CIRCADIAN CLOCK ASSOCIATED 1 like (CCA1L) proteins are important components that participate in plant growth and development, and now have been characterized in multiple plant species. However, information on ...

    Authors: Chenyang Liu, Qianqian Zhang, Jing Dong, Chunmei Cai, Hong Zhu and Shuai Li
    Citation: BMC Genomics 2022 23:374
  14. Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight int...

    Authors: Yao Jiang, Xiaojin Li, Jiali Liu, Wei Zhang, Mei Zhou, Jieru Wang, Linqing Liu, Shiguang Su, Fuping Zhao, Hongquan Chen and Chonglong Wang
    Citation: BMC Genomics 2022 23:373
  15. Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z...

    Authors: Sahbi Ferjaoui, Lamia Aouini, Rim B. Slimane, Karim Ammar, Suzanne Dreisigacker, Henk J. Schouten, Suraj Sapkota, Bochra A. Bahri, Sarrah Ben M’Barek, Richard G. F. Visser, Gert H. J. Kema and Sonia Hamza
    Citation: BMC Genomics 2022 23:372
  16. Cucurbita pepo is highly susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species cannot be considered as complete or broad-spectrum resistance. In this study, a source ...

    Authors: C. G. Amoroso, G. Andolfo, C. Capuozzo, A. Di Donato, C. Martinez, L. Tomassoli and M. R. Ercolano
    Citation: BMC Genomics 2022 23:371
  17. 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 23:370

    The original article was published in BMC Genomics 2022 23:206

  18. Drought stress is the most limiting factor for plant growth and crop production worldwide. As a major cereal crop, wheat is susceptible to drought. Thus, discovering and utilizing drought-tolerant gene resourc...

    Authors: Fengkun Lu, Wenjing Duan, Yue Cui, Junwei Zhang, Dong Zhu, Ming Zhang and Yueming Yan
    Citation: BMC Genomics 2022 23:369
  19. Numerous genome-wide association studies have been performed to understand the influence of genetic variation on type 2 diabetes etiology. Many identified risk variants are located in non-coding and intergenic...

    Authors: Gerard A. Bouland, Joline W. J. Beulens, Joey Nap, Arno R. van der Slik, Arnaud Zaldumbide, Leen M. ’t Hart and Roderick C. Slieker
    Citation: BMC Genomics 2022 23:368
  20. Baculoviruses act as effective biological control agents against the invasive pest Hyphantria cunea Drury. In this study, two Chinese Hyphantria cunea nucleopolyhedrovirus (HycuNPV) isolates, HycuNPV-BJ and HycuN...

    Authors: Xiaowei Peng, Wenying Zhang, Chengfeng Lei, Shuifa Min, Jia Hu, Qinghua Wang and Xiulian Sun
    Citation: BMC Genomics 2022 23:367
  21. Pichia pastoris (Komagataella phaffii) is a model organism widely used for the recombinant expression of eukaryotic proteins, and it can metabolize methanol as its sole carbon and energy source. Methanol is oxidi...

    Authors: Yi-fan Yu, Jiashuo Yang, Fengguang Zhao, Ying Lin and Shuangyan Han
    Citation: BMC Genomics 2022 23:366
  22. Escherichia coli carrying clinically important antimicrobial resistances [i.e., against extended-spectrum-beta-lactamases (ESBL)] are of high concern for human health and are increasingly detected worldwide. Worr...

    Authors: Katharina Juraschek, Janina Malekzadah, Burkhard Malorny, Annemarie Käsbohrer, Stefan Schwarz, Diana Meemken and Jens Andre Hammerl
    Citation: BMC Genomics 2022 23:365
  23. Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including...

    Authors: Weiwei Fu, Rui Wang, Naiyi Xu, Jinxin Wang, Ran Li, Hojjat Asadollahpour Nanaei, Qinghua Nie, Xin Zhao, Jianlin Han, Ning Yang and Yu Jiang
    Citation: BMC Genomics 2022 23:364
  24. Cervical artificial insemination (AI) with frozen-thawed semen results in unacceptably low pregnancy rates internationally. The exception is in Norway, where vaginal deposition of frozen-thawed semen to a natu...

    Authors: Laura Abril-Parreño, Kieran G. Meade, Anette Kristine Krogenæs, Xavier Druart, Paul Cormican and Sean Fair
    Citation: BMC Genomics 2022 23:363
  25. Multiple sclerosis (MS) is a debilitating immune-mediated disease of the central nervous system that affects over 2 million people worldwide, resulting in a heavy burden to families and entire communities. Und...

    Authors: Andi Liu, Astrid M. Manuel, Yulin Dai and Zhongming Zhao
    Citation: BMC Genomics 2022 23(Suppl 4):362

    This article is part of a Supplement: Volume 23 Supplement 4

  26. Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of...

    Authors: Fengyuan Huang, Li Xiao, Min Gao, Ethan J. Vallely, Kevin Dybvig, T. Prescott Atkinson, Ken B. Waites and Zechen Chong
    Citation: BMC Genomics 2022 23(Suppl 4):361

    This article is part of a Supplement: Volume 23 Supplement 4

  27. Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that are associated with complex human traits and diseases. miRNAs are single-stranded non-coding RNAs. In particular, geneti...

    Authors: Melinda Song, Jiaqi Yu, Binze Li, Julian Dong, Jeslyn Gao, Lulu Shang, Xiang Zhou and Yongsheng Bai
    Citation: BMC Genomics 2022 23(Suppl 4):360

    This article is part of a Supplement: Volume 23 Supplement 4

  28. Single-cell DNA sequencing is getting indispensable in the study of cell-specific cancer genomics. The performance of computational tools that tackle single-cell genome aberrations may be nevertheless underval...

    Authors: Xikang Feng and Lingxi Chen
    Citation: BMC Genomics 2022 23(Suppl 4):359

    This article is part of a Supplement: Volume 23 Supplement 4

  29. Yak estrus is a seasonal phenomenon, probably involving epigenetic regulation of synthesis and secretion of sex hormones as well as growth and development of follicles. N6-methyladenosine (m6A) is the most common...

    Authors: Shaoke Guo, Xingdong Wang, Mengli Cao, Xiaoyun Wu, Lin Xiong, Pengjia Bao, Min Chu, Chunnian Liang, Ping Yan, Jie Pei and Xian Guo
    Citation: BMC Genomics 2022 23:358
  30. The DoG (Delay of Germination1) family plays a key regulatory role in seed dormancy and germination. However, to date, there is no complete genomic overview of the DoG gene family of any economically valuable cro...

    Authors: Zhang Zhijun, Yu Peiyao, Huang Bing, Ma Ruifang, Kunnummal Kurungara Vinod and Muthusamy Ramakrishnan
    Citation: BMC Genomics 2022 23:357
  31. Alternative splicing (AS) increases the diversity of transcriptome and could fine-tune the function of genes, so that understanding the regulation of AS is vital. AS could be regulated by many different cis-regul...

    Authors: Cheng-Kai Shiau, Jia-Hsin Huang, Yu-Ting Liu and Huai-Kuang Tsai
    Citation: BMC Genomics 2022 22(Suppl 5):919

    This article is part of a Supplement: Volume 22 Supplement 5

  32. The mechanisms through which Mycobacterium tuberculosis evades immune surveillance during tuberculosis (TB) infection remain complex. Previous studies have found that Mycobacteria can manipulate the miRNAs of hos...

    Authors: Xuehua Zhan, Wenqi Yuan, Yueyong Zhou, Rong Ma and Zhaohui Ge
    Citation: BMC Genomics 2022 23:355
  33. We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondri...

    Authors: Dana Kristjansson, Jon Bohlin, Truc Trung Nguyen, Astanand Jugessur and Theodore G. Schurr
    Citation: BMC Genomics 2022 23:354
  34. The cotton leafworm, Spodoptera littoralis, is a highly polyphagous pest of many cultivated plants and crops in Africa and Europe. The genome of this pest will help us to further understand the molecular mechanis...

    Authors: Chao Wu, Lei Zhang, Bo Liu, Bojia Gao, Cong Huang, Ji Zhang, Minghui Jin, Hanyue Wang, Yan Peng, Annabel Rice, Esmat Hegazi, Kenneth Wilson, Pengjun Xu and Yutao Xiao
    Citation: BMC Genomics 2022 23:353
  35. Immune status in the tumor microenvironment is an important determinant of cancer progression and patient prognosis. Although a higher immune activity is often associated with a better prognosis, this trend is...

    Authors: Hitoshi Matsuo, Takashi Kamatani, Yu Hamba, Keith A. Boroevich and Tatsuhiko Tsunoda
    Citation: BMC Genomics 2022 23:351
  36. Lung cancer is the leading cause of cancer death in both men and women. The most common lung cancer subtype is non-small cell lung carcinoma (NSCLC) comprising about 85% of all cases. NSCLC can be further divi...

    Authors: Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin and Frank A. Feltus
    Citation: BMC Genomics 2022 23:350
  37. Real-time quantitative PCR is a widely used method for gene expression analyses in various organisms. Its accuracy mainly relies on the correct selection of reference genes. Any experimental plan involving rea...

    Authors: Federica Salatiello, Marco Gerdol, Alberto Pallavicini, Annamaria Locascio and Maria Sirakov
    Citation: BMC Genomics 2022 23:349
  38. CRISPR/Cas9-based genome-editing systems have been used to efficiently engineer livestock species with precise genetic alterations intended for biomedical and agricultural applications. Previously, we have suc...

    Authors: Shiwei Zhou, Peter Kalds, Qi Luo, Kexin Sun, Xiaoe Zhao, Yawei Gao, Bei Cai, Shuhong Huang, Qifang Kou, Bjoern Petersen, Yulin Chen, Baohua Ma and Xiaolong Wang
    Citation: BMC Genomics 2022 23:348
  39. Prenatal exposure to ethanol can cause fetal alcohol spectrum disorder (FASD), a prevalent, preventable pediatric disorder. Identifying genetic risk alleles for FASD is challenging since time, dose, and freque...

    Authors: Tatiana V. Morozova, Vijay Shankar, Rebecca A. MacPherson, Trudy F. C. Mackay and Robert R. H. Anholt
    Citation: BMC Genomics 2022 23:347
  40. The tomato (Solanum lycopersicum L.) is an economically valuable crop grown worldwide. Because the use of sterile males reduces the cost of F1 seed production, the innovation of male sterility is of great signifi...

    Authors: Huihui Bao, Yumei Ding, Fei Yang, Jie Zhang, Junjun Xie, Chongyan Zhao, Kanghua Du, Yawen Zeng, Kai Zhao, Zuosen Li and Zhengan Yang
    Citation: BMC Genomics 2022 23(Suppl 1):346

    This article is part of a Supplement: Volume 23 Supplement 1

  41. Pan-cancer studies have disclosed many commonalities and differences in mutations, copy number variations, and gene expression alterations among cancers. Some of these features are significantly associated wit...

    Authors: Po-Wen Wang, Yi-Hsun Su, Po-Hao Chou, Ming-Yueh Huang and Ting-Wen Chen
    Citation: BMC Genomics 2022 22(Suppl 5):918

    This article is part of a Supplement: Volume 22 Supplement 5

  42. Lung airway epithelial cells are part of innate immunity and the frontline of defense against bacterial infections. During infection, airway epithelial cells secrete proinflammatory mediators that participate ...

    Authors: Emel Sen-Kilic, Annalisa B. Huckaby, F. Heath Damron and Mariette Barbier
    Citation: BMC Genomics 2022 23:345
  43. The gaur (Bos gaurus) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, and is listed as vulnerable by the International Union for Conservation of Nature (IUCN).

    Authors: Wai Yee Low, Benjamin D. Rosen, Yan Ren, Derek M. Bickhart, Thu-Hien To, Fergal J. Martin, Konstantinos Billis, Tad S. Sonstegard, Shawn T. Sullivan, Stefan Hiendleder, John L. Williams, Michael P. Heaton and Timothy P. L. Smith
    Citation: BMC Genomics 2022 23:344
  44. The sustainable development of rice production is facing severe threats by a variety of pathogens, such as necrotrophic Rhizoctonia solani and hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo). Mining and applyi...

    Authors: Aijun Wang, Li Ma, Xinyue Shu, Yuqi Jiang, Juan Liang and Aiping Zheng
    Citation: BMC Genomics 2022 23:343
  45. The growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especia...

    Authors: Qiuxia Lei, Xin Hu, Haixia Han, Jie Wang, Wei Liu, Yan Zhou, Dingguo Cao, Fuwei Li and Jie Liu
    Citation: BMC Genomics 2022 23:342
  46. Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genom...

    Authors: Ana Corrochano-Fraile, Andrew Davie, Stefano Carboni and Michaël Bekaert
    Citation: BMC Genomics 2022 23:340

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