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  1. Berberine hydrochloride is the main effective component of Coptis spp. used in Chinese herbal medicine and its underlying molecular mechanisms, responsible for inducing effects in crustacean species, are not f...

    Authors: Tian-heng Gao, Ming-ming Han, Hui Zhou, Chen-xi Zhu, Ying Yang, Zakaria Zuraini, Yan-Xia Guo and Qi-chen Jiang
    Citation: BMC Genomics 2022 23:578
  2. Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging...

    Authors: Vladimir Mashanov, Denis Jacob Machado, Robert Reid, Cory Brouwer, Janice Kofsky and Daniel A. Janies
    Citation: BMC Genomics 2022 23:574
  3. Mammals rely on the circadian clock network to regulate daily systemic metabolism and physiological activities. The liver is an important peripheral organ in mammals, and it has a unique circadian rhythm regul...

    Authors: Yujia Chu, Jingjing Li, Lei Feng, Guoting Zhang, Hui Wu, Tinglei Jiang, Hui Wang and Jiang Feng
    Citation: BMC Genomics 2022 23:572
  4. Skeletal muscle tissue is among the largest organ systems in mammals, essential for survival and movement. Embryonic muscle development determines the quantity and quality of muscles after the birth of an indi...

    Authors: Jun’an Shi, Wendong Li, Anfang Liu, Lingtong Ren, Pusen Zhang, Ting Jiang, Yuqing Han and Lingbin Liu
    Citation: BMC Genomics 2022 23:571
  5. Saposhnikovia divaricata (Turcz.) Schischk. is a perennial herb whose dried roots are commonly used as a source of traditional medicines. To elucidate the organelle-genome-based phylogeny of Saposhnikovia species...

    Authors: Yang Ni, Jingling Li, Haimei Chen, Jingwen Yue, Pinghua Chen and Chang Liu
    Citation: BMC Genomics 2022 23:570
  6. To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here...

    Authors: David F. Nieuwenhuijse, Anne van der Linden, Robert H. G. Kohl, Reina S. Sikkema, Marion P. G. Koopmans and Bas B. Oude Munnink
    Citation: BMC Genomics 2022 23:569
  7. Brassinosteroids (BRs) are a group of essential steroid hormones involved in diverse developmental and physiological processes in plants. The Brassinazole-resistant 1 (BZR1) transcription factors are key compo...

    Authors: Chunliu Zuo, Lan Zhang, Xinyue Yan, Xinyue Guo, Qing Zhang, Songyang Li, Yanling Li, Wen Xu, Xiaoming Song, Jinpeng Wang and Min Yuan
    Citation: BMC Genomics 2022 23:568
  8. Acer pseudosieboldianum is a kind of excellent color-leafed plants, and well known for its red leaves in autumn. At the same time, A. pseudosieboldianum is one of the native tree species in the northeast of China...

    Authors: Jia-Lin Li, Zhuo Weng, Xin-Yu Li, Bo Xu, Yu-Fu Gao and Li-Ping Rong
    Citation: BMC Genomics 2022 23:567
  9. The genus Verbascum L. (Scrophulariaceae) is distributed in Africa, Europe, and parts of Asia, with the Mediterranean having the most species variety. Several researchers have already worked on the phylogenetic a...

    Authors: Xiang Dong, Elijah Mbandi Mkala, Elizabeth Syowai Mutinda, Jia-Xin Yang, Vincent Okelo Wanga, Millicent Akinyi Oulo, Victor Omondi Onjolo, Guang-Wan Hu and Qing-Feng Wang
    Citation: BMC Genomics 2022 23:566
  10. Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. Endogenous viral elements (EVE) play a role in this process probably via production of negative-sens...

    Authors: Suparat Taengchaiyaphum, Prapatsorn Wongkhaluang, Kanchana Sittikankaew, Nitsara Karoonuthaisiri, Timothy W. Flegel and Kallaya Sritunyalucksana
    Citation: BMC Genomics 2022 23:565
  11. Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH reg...

    Authors: Jan Berghöfer, Nadia Khaveh, Stefan Mundlos and Julia Metzger
    Citation: BMC Genomics 2022 23:564
  12. Type 2C protein phosphatase (PP2C) is a negative regulator of ABA signaling pathway, which plays important roles in stress signal transduction in plants. However, little research on the PP2C genes family of cucum...

    Authors: Guobin Zhang, Zeyu Zhang, Shilei Luo, Xia Li, Jian Lyu, Zeci Liu, Zilong Wan and Jihua Yu
    Citation: BMC Genomics 2022 23:563
  13. Transcriptome-wide association studies (TWASs) have shown great promise in interpreting the findings from genome-wide association studies (GWASs) and exploring the disease mechanisms, by integrating GWAS and e...

    Authors: Xiuyuan Jin, Liye Zhang, Jiadong Ji, Tao Ju, Jinghua Zhao and Zhongshang Yuan
    Citation: BMC Genomics 2022 23:562

    The Correction to this article has been published in BMC Genomics 2022 23:615

  14. Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome seq...

    Authors: Beatrice Kemilembe Mutayoba, Michael Hoelscher, Norbert Heinrich, Moses L. Joloba, Eligius Lyamuya, Andrew Martin Kilale, Nyagosya Segere Range, Bernard James Ngowi, Nyanda Elias Ntinginya, Saidi Mwinjuma Mfaume, Amani Wilfred, Basra Doulla, Johnson Lyimo, Riziki Kisonga, Amri Kingalu, Jupiter Marina Kabahita…
    Citation: BMC Genomics 2022 23:561
  15. Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimu...

    Authors: Zhengying Lu, Guo Yin, Mao Chai, Lu Sun, Hengling Wei, Jie Chen, Yufeng Yang, Xiaokang Fu and Shiyun Li
    Citation: BMC Genomics 2022 23:560
  16. Plants synthesize metabolites to adapt to a continuously changing environment. Metabolite biosynthesis often occurs in response to the tissue-specific combinatorial developmental cues that are transcriptionall...

    Authors: Xiaoyang Gao, Qixuan Su, Jing Li, Wenjing Yang, Baolin Yao, Jiawei Guo, Shengying Li and Changning Liu
    Citation: BMC Genomics 2022 23(Suppl 1):559

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

  17. Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism...

    Authors: Xue He, Hexing Wu, Yaping Ye, Xiaolin Gong and Baolong Bao
    Citation: BMC Genomics 2022 23:553
  18. The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end,...

    Authors: Zhi He, Zhijun Ma, Deying Yang, Qiqi Chen, Zhide He, Jiaxiang Hu, Faqiang Deng, Qian Zhang, Jiayang He, Lijuan Ye, Hongjun Chen, Liang He, Xiaoli Huang, Wei Luo, Shiyong Yang, Xiaobin Gu…
    Citation: BMC Genomics 2022 23:552
  19. In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold...

    Authors: Xiaolele Ma, Fangyuan Zhao, Kai Su, Hong Lin and Yinshan Guo
    Citation: BMC Genomics 2022 23:551
  20. The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indi...

    Authors: Yu Zhang, Qiaoqiao He, Xixi Zhou, Shimao Zheng, Yewen Wang, Peijiang Li and Yuexing Wang
    Citation: BMC Genomics 2022 23:550
  21. Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA g...

    Authors: Dili Lai, Xin Yao, Jun Yan, Anjing Gao, Hao Yang, Dabing Xiang, Jingjun Ruan, Yu Fan and Jianping Cheng
    Citation: BMC Genomics 2022 23:549
  22. Green-fleshed radish (Raphanus sativus L.) is an economically important root vegetable of the Brassicaceae family, and chlorophyll accumulates in its root tissues. It was reported that the basic helix-loop-helix ...

    Authors: Ruihua Wang, Yuanyuan Li, Minggang Gao, Min Han and Huilian Liu
    Citation: BMC Genomics 2022 23:548
  23. OSCA (hyperosmolality-gated calcium-permeable channel) is a calcium permeable cation channel protein that plays an important role in regulating plant signal transduction. It is involved in sensing changes in e...

    Authors: Shuang Miao, Fengshuo Li, Yang Han, Zhongtong Yao, Zeqian Xu, Xiuling Chen, Jiayin Liu, Yao Zhang and Aoxue Wang
    Citation: BMC Genomics 2022 23:547
  24. Population-scale expression profiling studies can provide valuable insights into biological and disease-underlying mechanisms. The availability of phenotypic traits is essential for studying clinical effects. ...

    Authors: Anna Niehues, Daniele Bizzarri, Marcel J.T. Reinders, P. Eline Slagboom, Alain J. van Gool, Erik B. van den Akker and Peter A.C. ’t Hoen
    Citation: BMC Genomics 2022 23:546
  25. Renal inflammation plays a crucial role during the progression of Chronic kidney disease (CKD), but there is limited research on hub genes involved in renal inflammation. Here, we aimed to explore the effects ...

    Authors: Jing Chen, Yuwei Liu, Shang Xia, Xujun Ye and Ling Chen
    Citation: BMC Genomics 2022 23:544
  26. The immune repertoires of mollusks beyond commercially important organisms such as the pacific oyster Crassostrea gigas or vectors for human pathogens like the bloodfluke planorb Biomphalaria glabrata are underst...

    Authors: Nicholas S. Kron
    Citation: BMC Genomics 2022 23:543
  27. Exposure to environmental mutagens increases the risk of cancer and genetic disorders. We used Duplex Sequencing (DS), a high-accuracy error-corrected sequencing technology, to analyze mutation induction acros...

    Authors: Danielle P. M. LeBlanc, Matthew Meier, Fang Yin Lo, Elizabeth Schmidt, Charles Valentine III, Andrew Williams, Jesse J. Salk, Carole L. Yauk and Francesco Marchetti
    Citation: BMC Genomics 2022 23:542
  28. Mymaridae is an ancient insect group and is a basal lineage of the superfamily Chalcidoidea. Species of Mymaridae have great potential for biological control. Anagrus nilaparvatae, a representative species of Mym...

    Authors: Ying Ma, Zixiao Guo, Liyang Wang, Bingyang Wang, Tingfa Huang, Bingjie Tang, Guren Zhang and Qiang Zhou
    Citation: BMC Genomics 2022 23:541
  29. Viola philippica Cav. is the only source plant of “Zi Hua Di Ding”, which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infect...

    Authors: Dong-Ling Cao, Xue-Jie Zhang, Shao-Qiu Xie, Shou-Jin Fan and Xiao-Jian Qu
    Citation: BMC Genomics 2022 23:540
  30. Long noncoding RNAs (lncRNAs) are emerging as a class of genes whose importance has yet to be fully realized. It is becoming clear that the primary function of lncRNAs is to regulate gene expression, and they ...

    Authors: Tadeusz J. Kaczynski, Elizabeth D. Au and Michael H. Farkas
    Citation: BMC Genomics 2022 23:539
  31. Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also pa...

    Authors: Hanqiu Ge, Jingjing Xu, Mingzhu Hua, Wenwen An, Junping Wu, Baohua Wang, Ping Li and Hui Fang
    Citation: BMC Genomics 2022 23:538
  32. The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices...

    Authors: Madison R. Turcotte, Joshua T. Smith, Jinfeng Li, Xinglu Zhang, Kristin L. Wolfe, Fengxiang Gao, Christopher S. Benton and Cheryl P. Andam
    Citation: BMC Genomics 2022 23:537
  33. Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees specie...

    Authors: Eduardo P. Cappa, Charles Chen, Jennifer G. Klutsch, Jaime Sebastian-Azcona, Blaise Ratcliffe, Xiaojing Wei, Letitia Da Ros, Aziz Ullah, Yang Liu, Andy Benowicz, Shane Sadoway, Shawn D. Mansfield, Nadir Erbilgin, Barb R. Thomas and Yousry A. El-Kassaby
    Citation: BMC Genomics 2022 23:536
  34. Phosphatidylethanolamine-binding protein (PEBP) is widely present in animals, plants, and microorganisms. Plant PEBP genes are mainly involved in flowering transition and nutritional growth. These genes have been...

    Authors: Jing He, Linxin Gu, Quanqin Tan, Yu Wang, Fanfan Hui, Xiaohong He, Pingan Chang, Daping Gong and Quan Sun
    Citation: BMC Genomics 2022 23:535
  35. Ribosomally-synthesized cyclic peptides are widely found in plants and exhibit useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the...

    Authors: Ziliang Song, Connor Burbridge, David J. Schneider, Timothy F. Sharbel and Martin J. T. Reaney
    Citation: BMC Genomics 2022 23:534
  36. GenoLab M is a recently developed next-generation sequencing (NGS) platform from GeneMind Biosciences. To establish the performance of GenoLab M, we present the first report to benchmark and compare the WGS an...

    Authors: Chaoyang Li, Xue Fan, Xin Guo, Yongfeng Liu, Miao Wang, Xiao Chao Zhao, Ping Wu, Qin Yan and Lei Sun
    Citation: BMC Genomics 2022 23:533
  37. Sugarcane is the most important sugar crop, contributing > 80% of global sugar production. High sucrose content is a key target of sugarcane breeding, yet sucrose improvement in sugarcane remains extremely slo...

    Authors: Ao-Mei Li, Zhong-Liang Chen, Cui-Xian Qin, Zi-Tong Li, Fen Liao, Ming-Qiao Wang, Prakash Lakshmanan, Yang-Rui Li, Miao Wang, You-Qiang Pan and Dong-Liang Huang
    Citation: BMC Genomics 2022 23:532
  38. This study aimed to identify long non-coding RNA (lncRNA) from the rumen tissue in dairy cattle, explore their features including expression and conservation levels, and reveal potential links between lncRNA a...

    Authors: Alexis Marceau, Yahui Gao, Ransom L. Baldwin VI, Cong-jun Li, Jicai Jiang, George E. Liu and Li Ma
    Citation: BMC Genomics 2022 23:531
  39. MYB transcription factor (TF) is one of the largest families of TFs in plants and play essential roles in plant growth and development, and is involved in responses to biological and abiotic stress. However, t...

    Authors: Hongjie Wang, Xiangli Yin, Dan Du, Zhongyi Liang, Zhenzhen Han, Hai Nian and Qibin Ma
    Citation: BMC Genomics 2022 23:529
  40. Adaptive thermogenesis by brown adipose tissue (BAT) is important to the maintenance of temperature in newborn mammals. Cold exposure activates gene expression and lipid metabolism to provide energy for BAT th...

    Authors: Xin Liu, Jing Tang, Runan Zhang, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Yan Wang, Jiaxue Cao, Li Li, Hongping Zhang and Linjie Wang
    Citation: BMC Genomics 2022 23:528
  41. Cashmere goats are a heterogeneous hairy mammal. The fineness of cashmere can affect its economic value. Therefore, in this study, we used transcriptome sequencing techniques to analyze the gene expression pro...

    Authors: Cuiling Wu, Jianying Li, Xinming Xu, Qi Xu, Chongkai Qin, Guifen Liu, Chen Wei, Guoping Zhang, Kechuan Tian and Xuefeng Fu
    Citation: BMC Genomics 2022 23:527
  42. In aquatic environments, pH, salinity, and ammonia concentration are extremely important for aquatic animals. NHE is a two-way ion exchange carrier protein, which can transport Na+ into cells and exchange out H+,...

    Authors: Jun Gao, Zhijuan Nie, Gangchun Xu and Pao Xu
    Citation: BMC Genomics 2022 23:526
  43. The transforming growth factor beta-1 (TGF β-1) cytokine exerts both pro-tumor and anti-tumor effects in carcinogenesis. An increasing body of literature suggests that TGF β-1 signaling outcome is partially depen...

    Authors: Jeremy W.K. Ng, Esther H.Q. Ong, Lisa Tucker-Kellogg and Greg Tucker-Kellogg
    Citation: BMC Genomics 2022 23(Suppl 1):525

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

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