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  1. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail ...

    Authors: Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang and Zhengli Liu

    Citation: BMC Genomics 2020 21:853

    Content type: Research article

    Published on:

  2. The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified ...

    Authors: Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang and Zhenhai Han

    Citation: BMC Genomics 2020 21:852

    Content type: Research article

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  3. Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the datab...

    Authors: Chang Ding and Lorenz Adrian

    Citation: BMC Genomics 2020 21:851

    Content type: Research article

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  4. Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is ...

    Authors: Ning Li, Ziwei Meng, Minjie Tao, Yueyuan Wang, Yulan Zhang, Shufen Li, Wujun Gao and Chuanliang Deng

    Citation: BMC Genomics 2020 21:850

    Content type: Research article

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  5. Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfor...

    Authors: E. A. Hisey, H. Hermans, Z. T. Lounsberry, F. Avila, R. A. Grahn, K. E. Knickelbein, S. A. Duward-Akhurst, M. E. McCue, T.S. Kalbfleisch, M. E. Lassaline, W. Back and R. R. Bellone

    Citation: BMC Genomics 2020 21:848

    Content type: Research article

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  6. Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with eith...

    Authors: Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz-Esser, Martin Wagner and Kathrin Rychli

    Citation: BMC Genomics 2020 21:847

    Content type: Research article

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  8. Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Disco...

    Authors: Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till and Hanna Bolibok-Brągoszewska

    Citation: BMC Genomics 2020 21:845

    Content type: Research article

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  9. After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial...

    Authors: Tatiana R. Feuerborn, Eleftheria Palkopoulou, Tom van der Valk, Johanna von Seth, Arielle R. Munters, Patrícia Pečnerová, Marianne Dehasque, Irene Ureña, Erik Ersmark, Vendela Kempe Lagerholm, Maja Krzewińska, Ricardo Rodríguez-Varela, Anders Götherström, Love Dalén and David Díez-del-Molino

    Citation: BMC Genomics 2020 21:844

    Content type: Methodology article

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  10. Post-traumatic osteoarthritis (PTOA) is a common and significant problem in equine athletes. It is a disease of the entire joint, with the synovium thought to be a key player in disease onset and progression d...

    Authors: Annette M. McCoy, Ann M. Kemper, Mary K. Boyce, Murray P. Brown and Troy N. Trumble

    Citation: BMC Genomics 2020 21:843

    Content type: Research article

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  11. Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important comp...

    Authors: Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang and San Ming Wang

    Citation: BMC Genomics 2020 21:842

    Content type: Research article

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  12. Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (...

    Authors: Guislaine Refrégier, Christophe Sola and Christophe Guyeux

    Citation: BMC Genomics 2020 21:841

    Content type: Research article

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  13. Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus)...

    Authors: Jiazhong Guo, Jie Zhong, George E. Liu, Liu Yang, Li Li, Guangling Chen, Tianzeng Song and Hongping Zhang

    Citation: BMC Genomics 2020 21:840

    Content type: Research article

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  15. Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-to...

    Authors: Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:838

    Content type: Research article

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  16. Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in ...

    Authors: Bianca Büttner, Vera Draba, Klaus Pillen, Günther Schweizer and Andreas Maurer

    Citation: BMC Genomics 2020 21:837

    Content type: Research article

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  17. Insect-killing fungal species, Beauveria bassiana, is as an environment-friendly pest management tool, and many isolates are on the track of industrialization. However, some of B. bassiana isolates show similar m...

    Authors: Sihyeon Kim, Jong Cheol Kim, Se Jin Lee, Mi Rong Lee, So Eun Park, Dongwei Li, Sehyeon Baek, Tae Young Shin and Jae Su Kim

    Citation: BMC Genomics 2020 21:836

    Content type: Research article

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  18. The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in pl...

    Authors: Xiu Feng, Yintao Jia, Ren Zhu, Kemao Li, Zhongzhi Guan and Yifeng Chen

    Citation: BMC Genomics 2020 21:835

    Content type: Research article

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  19. Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. gl...

    Authors: Chun-Ji Li, Die Zhao, Ping Cheng, Li Zheng and Guo-Hui Yu

    Citation: BMC Genomics 2020 21:834

    Content type: Research article

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  20. Primary hypoadrenocorticism (or Addison’s disease, AD) is an autoimmune disease that results in destruction of the adrenal cortex and consequent adrenal insufficiency. The disease has been described in purebre...

    Authors: Liza C. Gershony, Janelle M. Belanger, Marjo K. Hytönen, Hannes Lohi, Thomas R. Famula and Anita M. Oberbauer

    Citation: BMC Genomics 2020 21:833

    Content type: Research article

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  21. The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a ...

    Authors: Juan F. Guerra Maldonado, Antony T. Vincent, Martin Chenal and Frederic J. Veyrier

    Citation: BMC Genomics 2020 21:832

    Content type: Software

    Published on:

  22. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct...

    Authors: Caroline M. Stott and Louis-Marie Bobay

    Citation: BMC Genomics 2020 21:829

    Content type: Research article

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  23. Long term preservation of living ovarian tissues is a critical approach in human reproductive medicine as well as in the conservation of rare animal genotypes. Compared to single cell preservation, optimizatio...

    Authors: Olga Amelkina and Pierre Comizzoli

    Citation: BMC Genomics 2020 21:828

    Content type: Research article

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  26. Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CC...

    Authors: Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:825

    Content type: Research article

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  27. Periparturient cows release fatty acid reserves from adipose tissue (AT) through lipolysis in response to the negative energy balance induced by physiological changes related to parturition and the onset of la...

    Authors: David Salcedo-Tacuma, Jair Parales-Giron, Crystal Prom, Miguel Chirivi, Juliana Laguna, Adam L. Lock and G. Andres Contreras

    Citation: BMC Genomics 2020 21:824

    Content type: Research article

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  28. Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impac...

    Authors: Xiaofei Yang, Shenghan Gao, Tingjie Wang, Boyu Yang, Ningxin Dang and Kai Ye

    Citation: BMC Genomics 2020 21:823

    Content type: Methodology article

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  29. Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to...

    Authors: Andrew P. Wilkey, Anne V. Brown, Steven B. Cannon and Ethalinda K. S. Cannon

    Citation: BMC Genomics 2020 21:822

    Content type: Software

    Published on:

  30. Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by contro...

    Authors: Vatsala Koul, Divya Srivastava, Pushplata Prasad Singh and Mandira Kochar

    Citation: BMC Genomics 2020 21:821

    Content type: Research article

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  31. Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based ...

    Authors: Pratima Chapagain, Donald Walker, Tim Leeds, Beth M. Cleveland and Mohamed Salem

    Citation: BMC Genomics 2020 21:820

    Content type: Research article

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  32. The common cutworm, Spodoptera litura Fabricius is a leaf and fruit feeding generalist insect of the order Lepidoptera and a destructive agriculture pest. The broad host range of the herbivore is due to its abili...

    Authors: Vinod Kumar Prajapati, Mahendra Varma and Jyothilakshmi Vadassery

    Citation: BMC Genomics 2020 21:819

    Content type: Research article

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  33. Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dep...

    Authors: Julian Droste, Vera Ortseifen, Lena Schaffert, Marcus Persicke, Susanne Schneiker-Bekel, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2020 21:818

    Content type: Research article

    Published on:

  35. The gut microbiome can influence life history traits associated with host fitness such as fecundity and longevity. In most organisms, these two life history traits are traded-off, while they are positively lin...

    Authors: Matteo Antoine Negroni, Francisca H. I. D. Segers, Fanny Vogelweith and Susanne Foitzik

    Citation: BMC Genomics 2020 21:816

    Content type: Research article

    Published on:

  36. Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and fam...

    Authors: Astrid Tempestini, Gloria Massamba-N’Siala, Fanny Vermandele, Nicholas Beaudreau, Mathieu Mortz, France Dufresne and Piero Calosi

    Citation: BMC Genomics 2020 21:815

    Content type: Research article

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  37. Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human sal...

    Authors: Yuanmei Wang, Liying Liu, Min Li, Lili Lin, Pengcheng Su, Hui Tang, Xinzhong Fan and Xianyao Li

    Citation: BMC Genomics 2020 21:814

    Content type: Research article

    Published on:

  38. Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba). They are model organisms for studies in cellular and evolutionary...

    Authors: Tetsuro Kawano-Sugaya, Shinji Izumiyama, Yasuaki Yanagawa, Yumiko Saito-Nakano, Koji Watanabe, Seiki Kobayashi, Kumiko Nakada-Tsukui and Tomoyoshi Nozaki

    Citation: BMC Genomics 2020 21:813

    Content type: Research article

    Published on:

  39. Malonylation is a recently discovered post-translational modification that is associated with a variety of diseases such as Type 2 Diabetes Mellitus and different types of cancers. Compared with experimental i...

    Authors: Xin Liu, Liang Wang, Jian Li, Junfeng Hu and Xiao Zhang

    Citation: BMC Genomics 2020 21:812

    Content type: Methodology article

    Published on:

  40. Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids a...

    Authors: Guilherme Gainett, Jesús A. Ballesteros, Charlotte R. Kanzler, Jakob T. Zehms, John M. Zern, Shlomi Aharon, Efrat Gavish-Regev and Prashant P. Sharma

    Citation: BMC Genomics 2020 21:811

    Content type: Research article

    Published on:

  41. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Camilo Breton, Peter M. Clark, Lili Wang, Jenny A. Greig and James M. Wilson

    Citation: BMC Genomics 2020 21:810

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:239

  42. The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’...

    Authors: Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan and Jun Wu

    Citation: BMC Genomics 2020 21:809

    Content type: Research article

    Published on:

  44. Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilita...

    Authors: Chia-Chi Hsu, Shu-Yun Chen, Pei-Han Lai, Yu-Yun Hsiao, Wen-Chieh Tsai, Zhong-Jian Liu, Mei-Chu Chung, Olivier Panaud and Hong-Hwa Chen

    Citation: BMC Genomics 2020 21:807

    Content type: Research article

    Published on:

  45. Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughpu...

    Authors: Bronte Wen, Hyun Jun Jung, Lihe Chen, Fahad Saeed and Mark A. Knepper

    Citation: BMC Genomics 2020 21:806

    Content type: Software

    Published on:

  46. With declining wild fish populations, farmed salmon has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA). However, the introduction of plant oil in farmed salmon fe...

    Authors: Yang Jin, Alex K. Datsomor, Rolf E. Olsen, Jon Olav Vik, Jacob S. Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge and Fabian Grammes

    Citation: BMC Genomics 2020 21:805

    Content type: Research article

    Published on:

  47. The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein transl...

    Authors: Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdul Latif Khan and Ahmed Al-Harrasi

    Citation: BMC Genomics 2020 21:804

    Content type: Research article

    Published on:

  48. The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in li...

    Authors: Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond and Gabriela Lobinska

    Citation: BMC Genomics 2020 21(Suppl 10):779

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  49. Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for furth...

    Authors: Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars and H. Peter Hofstee

    Citation: BMC Genomics 2020 21(Suppl 10):683

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  50. Regulatory hotspots are genetic variations that may regulate the expression levels of many genes. It has been of great interest to find those hotspots utilizing expression quantitative trait locus (eQTL) analy...

    Authors: Ju Hun Choi, Taegun Kim, Junghyun Jung and Jong Wha J. Joo

    Citation: BMC Genomics 2020 21(Suppl 10):616

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

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