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  1. Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 a...

    Authors: Qiuhong Xiong, Ning Song, Ping Li, Sarah Fischer, Roman Konertz, Prerana Wagle, Gernot Glöckner, Changxin Wu and Ludwig Eichinger
    Citation: BMC Genomics 2021 22:444
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:555

  2. An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. Th...

    Authors: Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen and Xueying Guan
    Citation: BMC Genomics 2021 22:443
    Content type: Research article Published on:

  3. Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other...

    Authors: Zhiyu Yu, Rudolph Fredua-Agyeman, Sheau-Fang Hwang and Stephen E. Strelkov
    Citation: BMC Genomics 2021 22:442
    Content type: Research Published on:

  4. Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and ...

    Authors: Liyuan Wang, Yawen Zhang, Bo Zhang, Haian Zhong, Yunfeng Lu and Hao Zhang
    Citation: BMC Genomics 2021 22:441
    Content type: Research Published on:

  5. Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic muta...

    Authors: Xue Lin, Yingying Hua, Shuanglin Gu, Li Lv, Xingyu Li, Pin Chen, Peng Dai, Yunyun Hu, Anna Liu and Jian Li
    Citation: BMC Genomics 2021 22:440
    Content type: Software Published on:

  6. B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as i...

    Authors: Zhen Feng, Mengyu Li, Yi Li, Xu Yang, Hengling Wei, Xiaokang Fu, Liang Ma, Jianhua Lu, Hantao Wang and Shuxun Yu
    Citation: BMC Genomics 2021 22:439
    Content type: Research Published on:

  7. Myofibrillar myopathy in humans causes protein aggregation, degeneration, and weakness of skeletal muscle. In horses, myofibrillar myopathy is a late-onset disease of unknown origin characterized by poor perfo...

    Authors: Zoë J. Williams, Deborah Velez-Irizarry, Keri Gardner and Stephanie J. Valberg
    Citation: BMC Genomics 2021 22:438
    Content type: Research Published on:

  8. Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for a...

    Authors: Tejaswi Yarra, Kirti Ramesh, Mark Blaxter, Anne Hüning, Frank Melzner and Melody S. Clark
    Citation: BMC Genomics 2021 22:437
    Content type: Research article Published on:

  9. Gene interaction patterns, including modules and motifs, can be used to identify cancer specific biomarkers and to reveal the mechanism of tumorigenesis. Most of the existing module network inferencing methods...

    Authors: Xinguo Lu, Fang Liu, Qiumai Miao, Ping Liu, Yan Gao and Keren He
    Citation: BMC Genomics 2021 22(Suppl 1):436
    Content type: Methodology Published on:

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

  10. Formation of triploid organism is useful in genetics and breeding. In this study, autotriploid Carassius auratus (3nRR, 3n = 150) was generated from Carassius auratus red var. (RCC, 2n = 100) (♀) and autotetraplo...

    Authors: Chongqing Wang, Xiang Luo, Huan Qin, Chun Zhao, Li Yang, Tingting Yu, Yuxin Zhang, Xu Huang, Xidan Xu, Qinbo Qin and Shaojun Liu
    Citation: BMC Genomics 2021 22:435
    Content type: Research Published on:

  12. Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reporte...

    Authors: Jinyu Zhang, Huanqing Xu, Yuming Yang, Xiangqian Zhang, Zhongwen Huang and Dan Zhang
    Citation: BMC Genomics 2021 22:433
    Content type: Research article Published on:

  13. Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these...

    Authors: Yao Hu, Stephanie A. Bien, Katherine K. Nishimura, Jeffrey Haessler, Chani J. Hodonsky, Antoine R. Baldassari, Heather M. Highland, Zhe Wang, Michael Preuss, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Mariaelisa Graff, Laura M. Huckins, Quan Sun, Ming-Huei Chen…
    Citation: BMC Genomics 2021 22:432
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:656

  14. Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, sh...

    Authors: Lingtong Ren, Anfang Liu, Qigui Wang, Honggan Wang, Deqiang Dong and Lingbin Liu
    Citation: BMC Genomics 2021 22:431
    Content type: Research article Published on:

  17. Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken li...

    Authors: Junxiao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li and Xiaojun Liu
    Citation: BMC Genomics 2021 22:428
    Content type: Research article Published on:

  18. Lettuce (Lactuca sativa L.), one of the most economically important leaf vegetables, exhibits early bolting under high-temperature conditions. Early bolting leads to loss of commodity value and edibility, leading...

    Authors: Jing-hong Hao, He-Nan Su, Li-li Zhang, Chao-jie Liu, Ying-yan Han, Xiao-xiao Qin and Shuang-xi Fan
    Citation: BMC Genomics 2021 22:427
    Content type: Research article Published on:

  19. Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish...

    Authors: Xiaofei Yu, Hendrik-Jan Megens, Samuel Bekele Mengistu, John W. M. Bastiaansen, Han A. Mulder, John A. H. Benzie, Martien A. M. Groenen and Hans Komen
    Citation: BMC Genomics 2021 22:426
    Content type: Research article Published on:

  20. The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in respon...

    Authors: Geneviève Bart, Daniel Fischer, Anatoliy Samoylenko, Artem Zhyvolozhnyi, Pavlo Stehantsev, Ilkka Miinalainen, Mika Kaakinen, Tuomas Nurmi, Prateek Singh, Susanna Kosamo, Lauri Rannaste, Sirja Viitala, Jussi Hiltunen and Seppo J Vainio
    Citation: BMC Genomics 2021 22:425
    Content type: Research Published on:

  21. Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding no...

    Authors: Yong-Chao Xu, Jie Zhang, Dong-Yan Zhang, Ying-Hui Nan, Song Ge and Ya-Long Guo
    Citation: BMC Genomics 2021 22:424
    Content type: Research Published on:

  22. The study of protein complexes and protein functional modules has become an important method to further understand the mechanism and organization of life activities. The clustering algorithms used to analyze t...

    Authors: Zihao Zhao, Wenjun Xu, Aiwen Chen, Yueyue Han, Shengrong Xia, ChuLei Xiang, Chao Wang, Jun Jiao, Hui Wang, Xiaohui Yuan and Lichuan Gu
    Citation: BMC Genomics 2021 22:423
    Content type: Research Published on:

  23. Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, An...

    Authors: Melina Campos, Luisa D. P. Rona, Katie Willis, George K. Christophides and Robert M. MacCallum
    Citation: BMC Genomics 2021 22:422
    Content type: Research article Published on:

  24. Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distr...

    Authors: Yi Lei, Yu Zhou, Megan Price and Zhaobin Song
    Citation: BMC Genomics 2021 22:421
    Content type: Research Published on:

  25. Single-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many sc...

    Authors: Xinlei Wang, Lei Yu and Angela Ruohao Wu
    Citation: BMC Genomics 2021 22:420
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:554

  26. Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies ar...

    Authors: Stefan Kurtenbach, Anthony M. Cruz, Daniel A. Rodriguez, Michael A. Durante and J. William Harbour
    Citation: BMC Genomics 2021 22:419
    Content type: Software Published on:

  27. The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as ...

    Authors: Stanley Pang, Denise A Daley, Shafi Sahibzada, Shakeel Mowlaboccus, Marc Stegger and Geoffrey W Coombs
    Citation: BMC Genomics 2021 22:418
    Content type: Research article Published on:

  28. Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal p...

    Authors: Yu Du, Yong Wang, Qing Xu, Jiangjiang Zhu and Yaqiu Lin
    Citation: BMC Genomics 2021 22:417
    Content type: Research Published on:

  29. Copper was used for many years in aquaculture operations as an effective algaecide or a parasite treatment of fish. It is an essential nutrient with numerous functions in organisms, but is toxic at high concen...

    Authors: Wenjie Jin, Zixuan Li, Fengxia Ran, Shen Huang, Kefan Huo, Jianjuan Li, Qingshuo Han, Guojie Wang, Zhenji Wang, Shenlong Jian, Kemao Li and Changzhong Li
    Citation: BMC Genomics 2021 22:416
    Content type: Research article Published on:

  30. Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been...

    Authors: Yu Fan, Hao Yang, Dili Lai, Ailing He, Guoxing Xue, Liang Feng, Long Chen, Xiao-bin Cheng, Jingjun Ruan, Jun Yan and Jianping Cheng
    Citation: BMC Genomics 2021 22:415
    Content type: Research Published on:

  31. Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multipl...

    Authors: Danny Bergeron, Cédric Laforest, Stacey Carpentier, Annabelle Calvé, Étienne Fafard-Couture, Gabrielle Deschamps-Francoeur and Michelle S. Scott
    Citation: BMC Genomics 2021 22:414
    Content type: Research Published on:

  32. The spleen is the largest secondary lymphoid organ and the main site where stress erythropoiesis occurs. It is known that hypoxia triggers the expansion of erythroid progenitors; however, its effects on spleni...

    Authors: Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiangwen Chi and Tongzuo Zhang
    Citation: BMC Genomics 2021 22:413
    Content type: Research Published on:

  33. The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emergin...

    Authors: Sébastien Riquier, Marc Mathieu, Chloé Bessiere, Anthony Boureux, Florence Ruffle, Jean-Marc Lemaitre, Farida Djouad, Nicolas Gilbert and Thérèse Commes
    Citation: BMC Genomics 2021 22:412
    Content type: Research article Published on:

  34. Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans and the handling or consumption of contaminated poultry meat is a key source of infection. Selective breeding of poultry that exhib...

    Authors: Kay M. Russell, Jacqueline Smith, Abi Bremner, Cosmin Chintoan-Uta, Lonneke Vervelde, Androniki Psifidi and Mark P. Stevens
    Citation: BMC Genomics 2021 22:411
    Content type: Research Published on:

  35. Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unkn...

    Authors: Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou and Yun Zheng
    Citation: BMC Genomics 2021 22(Suppl 3):405
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  36. Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimat...

    Authors: Lily D. Peck, Reuben W. Nowell, Julie Flood, Matthew J. Ryan and Timothy G. Barraclough
    Citation: BMC Genomics 2021 22:404
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:514

  37. There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic difference...

    Authors: Ruijie Liu, Rick Tearle, Wai Yee Low, Tong Chen, Dana Thomsen, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams
    Citation: BMC Genomics 2021 22:410
    Content type: Research Published on:

  38. Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development a...

    Authors: Vittoria Roncalli, Matthew C. Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline and Petra H. Lenz
    Citation: BMC Genomics 2021 22:409
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:659

  39. Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature w...

    Authors: Dessie Salilew-Wondim, Dawit Tesfaye, Franca Rings, Eva Held-Hoelker, Dennis Miskel, Marc-Andre Sirard, Ernst Tholen, Karl Schellander and Michael Hoelker
    Citation: BMC Genomics 2021 22:408
    Content type: Research Published on:

  40. Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretati...

    Authors: Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S. Cram and Yu Zhang
    Citation: BMC Genomics 2021 22:407
    Content type: Software Published on:

  41. Chlamydia psittaci is an avian pathogen that can cause lethal human infections. Diagnosis of C. psittaci pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic tech...

    Authors: Kaiying Wang, Xiong Liu, Huiying Liu, Peihan Li, Yanfeng Lin, Dongdong Yin, Lang Yang, Jinhui Li, Shenlong Li, Leili Jia, Changqing Bai, Yongqiang Jiang, Peng Li and Hongbin Song
    Citation: BMC Genomics 2021 22:406
    Content type: Research article Published on:

  42. The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as An...

    Authors: So-Ra Han, Byeollee Kim, Jong Hwa Jang, Hyun Park and Tae-Jin Oh
    Citation: BMC Genomics 2021 22:403
    Content type: Research Published on:

  43. Observational studies have identified various associations between neuroimaging alterations and neuropsychiatric disorders. However, whether such associations could truly reflect causal relations remains still...

    Authors: Weichen Song, Wei Qian, Weidi Wang, Shunying Yu and Guan Ning Lin
    Citation: BMC Genomics 2021 22(Suppl 3):342
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  45. Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characte...

    Authors: Noah DeWitt, Mohammed Guedira, Edwin Lauer, J. Paul Murphy, David Marshall, Mohamed Mergoum, Jerry Johnson, James B. Holland and Gina Brown-Guedira
    Citation: BMC Genomics 2021 22:402
    Content type: Research article Published on:

  46. Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed w...

    Authors: Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Jinping Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang and Lizhi Lu
    Citation: BMC Genomics 2021 22:401
    Content type: Research article Published on:

  47. Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment an...

    Authors: Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer and Rita V. M. Rio
    Citation: BMC Genomics 2021 22:400
    Content type: Research article Published on:

  48. Pair bonding with a reproductive partner is rare among mammals but is an important feature of human social behavior. Decades of research on monogamous prairie voles (Microtus ochrogaster), along with comparative ...

    Authors: Joel A. Tripp, Alejandro Berrio, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young and Steven M. Phelps
    Citation: BMC Genomics 2021 22:399
    Content type: Research Published on:

  49. A conformational epitope (CE) is composed of neighboring amino acid residues located on an antigenic protein surface structure. CEs bind their complementary paratopes in B-cell receptors and/or antibodies. An ...

    Authors: Ying-Tsang Lo, Tao-Chuan Shih, Tun-Wen Pai, Li-Ping Ho, Jen-Leih Wu and Hsin-Yiu Chou
    Citation: BMC Genomics 2021 22(Suppl 2):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 2

  50. Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled...

    Authors: Wilson Nandolo, Gábor Mészáros, Maria Wurzinger, Liveness J. Banda, Timothy N. Gondwe, Henry A. Mulindwa, Helen N. Nakimbugwe, Emily L. Clark, M. Jennifer Woodward-Greene, Mei Liu, George E. Liu, Curtis P. Van Tassell, Benjamin D. Rosen and Johann Sölkner
    Citation: BMC Genomics 2021 22:398
    Content type: Research article Published on:

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BMC Genomics

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