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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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

  14. Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reserv...

    Authors: Marina Athanasouli and Christian Rödelsperger
    Citation: BMC Genomics 2022 23:523
  15. African swine fever (ASF) is a lethal hemorrhagic disease affecting domestic pigs resulting in up to 100% mortality rates caused by the ASF virus (ASFV). The locally-adapted pigs in South-western Kenya have be...

    Authors: Eunice Magoma Machuka, John Juma, Anne Wangari Thairu Muigai, Joshua Oluoch Amimo, Roger Pelle and Edward Okoth Abworo
    Citation: BMC Genomics 2022 23:522
  16. Conogethes pinicolalis has been thought as a Pinaceae-feeding variant of the yellow peach moth, Conogethes punctiferalis. The divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis has been rep...

    Authors: Dapeng Jing, Sivaprasath Prabu, Tiantao Zhang, Shuxiong Bai, Kanglai He, Yongjun Zhang and Zhenying Wang
    Citation: BMC Genomics 2022 23:521
  17. Genetic evolution of Rift Valley fever virus (RVFV) in Africa has been shaped mainly by environmental changes such as abnormal rainfall patterns and climate change that has occurred over the last few decades. ...

    Authors: John Juma, Vagner Fonseca, Samson L. Konongoi, Peter van Heusden, Kristina Roesel, Rosemary Sang, Bernard Bett, Alan Christoffels, Tulio de Oliveira and Samuel O. Oyola
    Citation: BMC Genomics 2022 23:520
  18. Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regu...

    Authors: Keren Long, Duo Su, Xiaokai Li, Hengkuan Li, Sha Zeng, Yu Zhang, Zhining Zhong, Yu Lin, Xuemin Li, Lu Lu, Long Jin, Jideng Ma, Qianzi Tang and Mingzhou Li
    Citation: BMC Genomics 2022 23:519
  19. Group A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and anim...

    Authors: Han Wu, Bingzhe Li, Ziping Miao, Linjie Hu, Lu Zhou and Yihan Lu
    Citation: BMC Genomics 2022 23:518
  20. Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled...

    Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, Robert D. Schnabel, Jared E. Decker and Christopher M. Seabury
    Citation: BMC Genomics 2022 23:517
  21. The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this...

    Authors: D. De Panis, H. Dopazo, E. Bongcam-Rudloff, A. Conesa and E. Hasson
    Citation: BMC Genomics 2022 23:515
  22. Ammonium is an important raw material for biomolecules and life activities, and the toxicity of ammonium is also an important ecological and agricultural issue. Ammonium toxicity in yeast has only recently bee...

    Authors: Wenhao Fu, Xiuling Cao, Tingting An, Huihui Zhao, Jie Zhang, Danqi Li, Xuejiao Jin and Beidong Liu
    Citation: BMC Genomics 2022 23:514
  23. With the emergence and spread of SARS-CoV-2 variants, genomic epidemiology and surveillance have proven invaluable tools for variant tracking. Here, we analyzed SARS-CoV-2 samples collected from personnel loca...

    Authors: Irina Maljkovic Berry, Jun Hang, Christian Fung, Yu Yang, Marcus Chibucos, Adam Pollio, Jay Gandhi, Tao Li, Matthew A. Conte, Grace M. Lidl, Jay A. Johannigman and Heather Friberg
    Citation: BMC Genomics 2022 23:513
  24. Chinese chestnut is an economically important tree species whose yield and quality are seriously affected by red spider attack. Tannins is one of the most important class secondary metabolites in plants, and i...

    Authors: Suying Li, Yanjiao Cui, Dan Liu, Zilong Zhao, Jing Zhang and Zhengli Liu
    Citation: BMC Genomics 2022 23:512
  25. Bulbus Fritillariae Cirrhosae (BFC) is an endangered high-altitude medicine and food homology plant with anti-tumor, anti-asthmatic, and antitussive activities as it contains a variety of active ingredients, espe...

    Authors: Qiuxia Lu, Rui Li, Jiaqing Liao, Yuqin Hu, Yundong Gao, Mingcheng Wang, Jian Li and Qi Zhao
    Citation: BMC Genomics 2022 23:511
  26. The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic a...

    Authors: Nadia B. Olivero, Ana S. Gonzalez-Reiche, Viviana E. Re, Gonzalo M. Castro, María B. Pisano, Paola Sicilia, María G. Barbas, Zenab Khan, Adriana van de Guchte, Jayeeta Dutta, Paulo R. Cortes, Mirelys Hernandez-Morfa, Victoria E. Zappia, Lucia Ortiz, Ginger Geiger, Daniela Rajao…
    Citation: BMC Genomics 2022 23:510
  27. Duck plague virus (DPV), belonging to herpesviruses, is a linear double-stranded DNA virus. There are many reports about the outbreak of the duck plague in a variety of countries, which caused huge economic lo...

    Authors: Ziyu Wu, Yue Zeng, Anchun Cheng, Anyang Sun, Mingshu Wang, Shun Chen, Mafeng Liu, Dekang Zhu, Xinxin Zhao, Ying Wu, Qiao Yang, Shaqiu Zhang, Juan Huang, Xumin Ou, Qun Gao, Sai Mao…
    Citation: BMC Genomics 2022 23:509
  28. The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biod...

    Authors: Brianna L. Boss, Abanoub E. Wanees, Shari J. Zaslow, Tyler G. Normile and Javier A. Izquierdo
    Citation: BMC Genomics 2022 23:508
  29. Changes in the abundance of ovarian proteins play a key role in the regulation of reproduction. However, to date, no studies have investigated such changes in pubescent goats. Herein we applied isobaric tags f...

    Authors: Ping Qin, Jing Ye, Xinbao Gong, Xu Yan, Maosen Lin, Tao Lin, Tong Liu, Hailing Li, Xiujuan Wang, Yanyun Zhu, Xiaoqian Li, Ya Liu, Yunsheng Li, Yinghui Ling, Xiaorong Zhang and Fugui Fang
    Citation: BMC Genomics 2022 23:507
  30. The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of ...

    Authors: Weian Du, Domenico Giosa, Junkang Wei, Letterio Giuffrè, Ge Shi, Lamya El Aamri, Enrico D’Alessandro, Majida Hafidi, Sybren de Hoog, Orazio Romeo and Huaiqiu Huang
    Citation: BMC Genomics 2022 23:506
  31. The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well as for evolutionary and comparative genomics. The improvement of long-read s...

    Authors: Istvan Nagy, Elisabeth Veeckman, Chang Liu, Michiel Van Bel, Klaas Vandepoele, Christian Sig Jensen, Tom Ruttink and Torben Asp
    Citation: BMC Genomics 2022 23:505
  32. The filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key ge...

    Authors: Tianxiunan Pu, Zejun Mo, Long Su, Jing Yang, Ke Wan, Linqi Wang, Renxiang Liu and Yang Liu
    Citation: BMC Genomics 2022 23:503
  33. Authors: Claude Rispe, Caroline Hervet, Nathalie de la Cotte, Romain Daveu, Karine Labadie, Benjamin Noel, Jean-Marc Aury, Steeve Thany, Emiliane Taillebois, Alison Cartereau, Anaïs Le Mauf, Claude L. Charvet, Clément Auger, Elise Courtot, Cédric Neveu and Olivier Plantard
    Citation: BMC Genomics 2022 23:502

    The original article was published in BMC Genomics 2022 23:463

  34. Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH)...

    Authors: Julie Colpitts, Philip Dunstan McLoughlin and Jocelyn Poissant
    Citation: BMC Genomics 2022 23:501
  35. The cultivated peanut (Arachis hypogaea L., AABB) is an allotetraploid hybrid between two diploid peanuts, A. duranensis (AA genome) and A. ipaensis (BB genome). Miniature inverted-repeat transposable elements (M...

    Authors: Yanyan Tang, Xiaoting Li, Changli Hu, Xiaochen Qiu, Jingjing Li, Xin Li, Hong Zhu, Jingshan Wang, Jiongming Sui and Lixian Qiao
    Citation: BMC Genomics 2022 23:500
  36. The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in...

    Authors: Kuiyin Li, Yue Fan, Guangyi Zhou, Xiaojuan Liu, Songshu Chen, Xiangcai Chang, Wenqiang Wu, Lili Duan, Maoxing Yao, Rui Wang, Zili Wang, Mingfang Yang, Yanqing Ding, Mingjian Ren, Yu Fan and Liyi Zhang
    Citation: BMC Genomics 2022 23:499
  37. The impact of S. enterica colonization in cattle is highly variable and often serovar-dependent. The aim of this study was to compare the global transcriptomes of highly pathogenic bovine-adapted S. enterica sero...

    Authors: Serajus Salaheen, Seon Woo Kim, Bradd J. Haley and Jo Ann S. Van Kessel
    Citation: BMC Genomics 2022 23:498
  38. Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it...

    Authors: Yuki Iwasaki, Toshimichi Ikemura, Kennosuke Wada, Yoshiko Wada and Takashi Abe
    Citation: BMC Genomics 2022 23:497
  39. Reliable and effective label-free quantification (LFQ) analyses are dependent not only on the method of data acquisition in the mass spectrometer, but also on the downstream data processing, including software...

    Authors: Zeeshan Hamid, Kip D. Zimmerman, Hector Guillen-Ahlers, Cun Li, Peter Nathanielsz, Laura A. Cox and Michael Olivier
    Citation: BMC Genomics 2022 23:496
  40. Shigella specie is a globally important intestinal pathogen disseminated all over the world. In this study we analyzed the genome and the proteomic component of two Shigella flexneri 2a clinical isolates, collect...

    Authors: Mónica F. Torrez Lamberti, Lucrecia C. Terán, Fabián E. Lopez, María de las Mercedes Pescaretti and Mónica A. Delgado
    Citation: BMC Genomics 2022 23:495
  41. Maternal recognition is the crucial step for establishing pregnancy in cattle. This study aims to identify endometrial genes and biological pathways involved in the maternal recognition of pregnancy. Caruncula...

    Authors: Bindu Adhikari, Chin N. Lee, Vedbar S. Khadka, Youping Deng, Glen Fukumoto, Mark Thorne, Kyle Caires, Jenee Odani and Birendra Mishra
    Citation: BMC Genomics 2022 23:494
  42. To detect changes in biological processes, samples are often studied at several time points. We examined expression data measured at different developmental stages, or more broadly, historical data. Hence, the...

    Authors: Miriam Sieg, Lina Katrin Sciesielski, Karin Michaela Kirschner and Jochen Kruppa
    Citation: BMC Genomics 2022 23:491
  43. The evolution of parasites is often directly affected by the host's environment. Studies on the evolution of the same parasites in different hosts are of great interest and are highly relevant to our understan...

    Authors: Lei Han, Tianming Lan, Yaxian Lu, Mengchao Zhou, Haimeng Li, Haorong Lu, Qing Wang, Xiuyun Li, Shan Du, Chunyu Guan, Yong Zhang, Sunil Kumar Sahu, Puyi Qian, Shaofang Zhang, Hongcheng Zhou, Wei Guo…
    Citation: BMC Genomics 2022 23:489

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