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Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

Page 1 of 19

  1. Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the p...

    Authors: Yang Yang, Huiqiang Zhou, Liping Hou, Ke Xing and Hu Shu

    Citation: BMC Genomics 2019 20:938

    Content type: Research article

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  2. MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aur...

    Authors: Shaoyang Ma, Chao Tong, Eveline M. Ibeagha-Awemu and Xin Zhao

    Citation: BMC Genomics 2019 20:934

    Content type: Research article

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  3. Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population di...

    Authors: Qiong Wang, Yaxiong Jia, Yuan Wang, Zhihua Jiang, Xiang Zhou, Zebin Zhang, Changsheng Nie, Junying Li, Ning Yang and Lujiang Qu

    Citation: BMC Genomics 2019 20:933

    Content type: Research article

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  4. Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide...

    Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker and Christopher M. Seabury

    Citation: BMC Genomics 2019 20:926

    Content type: Research article

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  5. Compensatory growth refers to the phenomenon in which organisms grow faster after the improvement of an adverse environment and is thought to be an adaptive evolution to cope with the alleviation of the hostil...

    Authors: Jirong Jia, Jingkai Qin, Xi Yuan, Zongzhen Liao, Jinfeng Huang, Bin Wang, Caiyun Sun and Wensheng Li

    Citation: BMC Genomics 2019 20:919

    Content type: Research article

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  6. Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the s...

    Authors: Abdolrahman Khezri, Birgitte Narud, Else-Berit Stenseth, Anders Johannisson, Frøydis Deinboll Myromslien, Ann Helen Gaustad, Robert C. Wilson, Robert Lyle, Jane M. Morrell, Elisabeth Kommisrud and Rafi Ahmad

    Citation: BMC Genomics 2019 20:897

    Content type: Research article

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  8. DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others.

    Authors: Shuli Liu, Lingzhao Fang, Yang Zhou, Daniel J.A. Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Cong-jun Li, Ying Yu, Li Ma, Shengli Zhang and George E. Liu

    Citation: BMC Genomics 2019 20:888

    Content type: Research article

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  9. The function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we ...

    Authors: Wanbin Hu, Shuxin Yang, Yasuhito Shimada, Magnus Münch, Rubén Marín-Juez, Annemarie H. Meijer and Herman P. Spaink

    Citation: BMC Genomics 2019 20:878

    Content type: Research article

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  10. The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restorat...

    Authors: Íria Gabriela Dias dos Santos, Tiago Antônio de Oliveira Mendes, Gerluza Aparecida Borges Silva, Amanda Maria Sena Reis, Cláudia Barros Monteiro-Vitorello, Patricia Dayane Carvalho Schaker, Roberto Hirochi Herai, André Brait Carneiro Fabotti, Luiz Lehmann Coutinho and Erika Cristina Jorge

    Citation: BMC Genomics 2019 20:866

    Content type: Research article

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  11. Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This ...

    Authors: Lu Liu, Xiaojing Liu, Huanxian Cui, Ranran Liu, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2019 20:863

    Content type: Research article

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  12. The ureagenesis plays a central role in the homeostatic control of nitrogen metabolism. This process occurs in the liver, the key metabolic organ in the maintenance of energy homeostasis in the body. To date, ...

    Authors: Zhongyan Lu, Zhihui Xu, Zanming Shen, Hong Shen and Jörg R. Aschenbach

    Citation: BMC Genomics 2019 20:854

    Content type: Research article

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  13. Subfertility is a major issue facing the dairy industry as the average US Holstein cow conception rate (CCR) is approximately 35%. The genetics underlying the physiological processes responsible for CCR, the p...

    Authors: Jennifer N. Kiser, Erin Clancey, Joao G. N. Moraes, Joseph Dalton, Gregory W. Burns, Thomas E. Spencer and Holly L. Neibergs

    Citation: BMC Genomics 2019 20:840

    Content type: Research article

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  14. Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the br...

    Authors: Wenliang Yuan, Shouwen Jiang, Dan Sun, Zhichao Wu, Cai Wei, Chaoxu Dai, Linhua Jiang and Sihua Peng

    Citation: BMC Genomics 2019 20:830

    Content type: Research article

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  15. Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore mo...

    Authors: Jinghang Zhou, Liyuan Liu, Chunpeng James Chen, Menghua Zhang, Xin Lu, Zhiwu Zhang, Xixia Huang and Yuangang Shi

    Citation: BMC Genomics 2019 20:827

    Content type: Research article

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  16. At sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying he...

    Authors: Audrey Gloux, Michel J. Duclos, Aurélien Brionne, Marie Bourin, Yves Nys and Sophie Réhault-Godbert

    Citation: BMC Genomics 2019 20:821

    Content type: Research article

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  17. The brain plays a critical role in upstream regulation of processes central to mating effort, parental effort, and self-maintenance. For seasonally breeding animals, the brain is likely mediating trade-offs am...

    Authors: Alexandra B. Bentz, Douglas B. Rusch, Aaron Buechlein and Kimberly A. Rosvall

    Citation: BMC Genomics 2019 20:819

    Content type: Research article

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  18. The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same reg...

    Authors: M. Yaro, K. A. Munyard, E. Morgan, R. J. N. Allcock, M. J. Stear and D. M. Groth

    Citation: BMC Genomics 2019 20:816

    Content type: Research article

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  19. The study of the mechanisms controlling wound healing is an attractive area within the field of biology, with it having a potentially significant impact on the health sector given the current medical burden as...

    Authors: Pavel Abaffy, Silvie Tomankova, Ravindra Naraine, Mikael Kubista and Radek Sindelka

    Citation: BMC Genomics 2019 20:815

    Content type: Research article

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  20. Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However,...

    Authors: Xuelian Ma, Xiaomin Zhao, Kaili Wang, Xiaoyi Tang, Jianxiong Guo, Mi Mi, Yanping Qi, Lingling Chang, Yong Huang and Dewen Tong

    Citation: BMC Genomics 2019 20:806

    Content type: Research article

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  21. The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement call...

    Authors: Hairong Luo, Xiaoyu Kong, Shixi Chen and Wei Shi

    Citation: BMC Genomics 2019 20:792

    Content type: Research article

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  22. Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainb...

    Authors: Pratima Chapagain, Brock Arivett, Beth M. Cleveland, Donald M. Walker and Mohamed Salem

    Citation: BMC Genomics 2019 20:788

    Content type: Research article

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  23. Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hy...

    Authors: Jianjun Fu, Wenbin Zhu, Lanmei Wang, Mingkun Luo, Feibiao Song and Zaijie Dong

    Citation: BMC Genomics 2019 20:781

    Content type: Research article

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  24. Bovine viral diarrhoea virus (BVDV) is the member of the genus Pestivirus within the Flaviviridae family and responsible for severe economic losses in the cattle industry. BVDV can employ ‘infect-and-persist’ str...

    Authors: Cun Liu, Yanhan Liu, Lin Liang, Shangjin Cui and Yanming Zhang

    Citation: BMC Genomics 2019 20:774

    Content type: Research article

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  26. A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs ...

    Authors: María Gabián, Paloma Morán, Ana I. Fernández, Beatriz Villanueva, Amel Chtioui, Matthew P. Kent, Lara Covelo-Soto, Almudena Fernández and María Saura

    Citation: BMC Genomics 2019 20:764

    Content type: Research article

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  27. Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentia...

    Authors: Marina Solé, Michela Ablondi, Amrei Binzer-Panchal, Brandon D. Velie, Nina Hollfelder, Nadine Buys, Bart J. Ducro, Liesbeth François, Steven Janssens, Anouk Schurink, Åsa Viklund, Susanne Eriksson, Anders Isaksson, Hanna Kultima, Sofia Mikko and Gabriella Lindgren

    Citation: BMC Genomics 2019 20:759

    Content type: Research article

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  28. The distribution and deposition of fat tissue in different parts of the body are the key factors affecting the carcass quality and meat flavour of chickens. Intramuscular fat (IMF) content is an important fact...

    Authors: Meng Zhang, Fang Li, Xiang-fei Ma, Wen-ting Li, Rui-rui Jiang, Rui-li Han, Guo-xi Li, Yan-bin Wang, Zi-yi Li, Ya-dong Tian, Xiang-tao Kang and Gui-rong Sun

    Citation: BMC Genomics 2019 20:743

    Content type: Research article

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  29. Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of globin mRNA i...

    Authors: Kyu-Sang Lim, Qian Dong, Pamela Moll, Jana Vitkovska, Gregor Wiktorin, Stephanie Bannister, Dalia Daujotyte, Christopher K. Tuggle, Joan K. Lunney, Graham S. Plastow and Jack C. M. Dekkers

    Citation: BMC Genomics 2019 20:741

    Content type: Research article

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  30. Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of th...

    Authors: Zaira M. Estrada-Reyes, Yoko Tsukahara, Rodrigo R. Amadeu, Arthur L. Goetsch, Terry A. Gipson, Tilahun Sahlu, Richard Puchala, Zaisen Wang, Steve P. Hart and Raluca G. Mateescu

    Citation: BMC Genomics 2019 20:735

    Content type: Research article

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  31. More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian ...

    Authors: Linda Beauclair, Christelle Ramé, Peter Arensburger, Benoît Piégu, Florian Guillou, Joëlle Dupont and Yves Bigot

    Citation: BMC Genomics 2019 20:734

    Content type: Research article

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  32. It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs’ immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RF...

    Authors: Haibo Liu, Kristina M. Feye, Yet T. Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Dekkers, Nicholas K. Gabler and Christopher K. Tuggle

    Citation: BMC Genomics 2019 20:728

    Content type: Research article

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  33. The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and th...

    Authors: D. C. Purfield, R. D. Evans and D. P. Berry

    Citation: BMC Genomics 2019 20:720

    Content type: Research article

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  34. Genomic evaluation is usually based on a set of markers assumed to be linked with causal mutations. Selection and precise management of major genes and the remaining polygenic component might be improved by in...

    Authors: Claire Oget, Marc Teissier, Jean-Michel Astruc, Gwenola Tosser-Klopp and Rachel Rupp

    Citation: BMC Genomics 2019 20:719

    Content type: Research article

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  35. A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic reg...

    Authors: Michela Ablondi, Åsa Viklund, Gabriella Lindgren, Susanne Eriksson and Sofia Mikko

    Citation: BMC Genomics 2019 20:717

    Content type: Research article

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  36. In mammals, hypohidrotic ectodermal dysplasia (HED) is a genetic disorder that is characterized by sparse hair, tooth abnormalities, and defects in cutaneous glands. Only four genes, EDA, EDAR, EDARADD and WNT10A

    Authors: Clémentine Escouflaire, Emmanuelle Rebours, Mathieu Charles, Sébastien Orellana, Margarita Cano, Julie Rivière, Cécile Grohs, Hélène Hayes and Aurélien Capitan

    Citation: BMC Genomics 2019 20:715

    Content type: Research article

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  37. Subfertility decreases the efficiency of the cattle industry because artificial insemination employs spermatozoa from a single bull to inseminate thousands of cows. Variation in bull fertility has been demonst...

    Authors: E. B. Menezes, A. L. C. Velho, F. Santos, T. Dinh, A. Kaya, E. Topper, A. A. Moura and E. Memili

    Citation: BMC Genomics 2019 20:714

    Content type: Research article

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  38. Successful social behavior requires real-time integration of information about the environment, internal physiology, and past experience. The molecular substrates of this integration are poorly understood, but...

    Authors: Austin T. Hilliard, Dan Xie, Zhihai Ma, Michael P. Snyder and Russell D. Fernald

    Citation: BMC Genomics 2019 20:699

    Content type: Research article

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  40. Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperatu...

    Authors: Veronika N. Laine, Irene Verhagen, A. Christa Mateman, Agata Pijl, Tony D. Williams, Phillip Gienapp, Kees van Oers and Marcel E. Visser

    Citation: BMC Genomics 2019 20:693

    Content type: Research article

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  41. Pekin duck is an important animal model for its ability for fat synthesis and deposition. However, transcriptional dynamic regulation of adipose differentiation driven by complex signal cascades remains largel...

    Authors: Zheng Wang, Zhong-Tao Yin, Fan Zhang, Xiao-Qin Li, Si-Rui Chen, Ning Yang, Tom E. Porter and Zhuocheng Hou

    Citation: BMC Genomics 2019 20:688

    Content type: Research article

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  42. We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet inc...

    Authors: Monique L. van Hoek, M. Dennis Prickett, Robert E. Settlage, Lin Kang, Pawel Michalak, Kent A. Vliet and Barney M. Bishop

    Citation: BMC Genomics 2019 20:684

    Content type: Research article

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  43. Porcine embryos undergo rapid differentiation and expansion between Days 8 and 12 before attaching to the maternal uterine epithelial surface after Day 13. It is known that maternal recognition of pregnancy an...

    Authors: Shuqin Zeng, Jochen Bick, David Kradolfer, Johannes Knubben, Veronika L. Flöter, Stefan Bauersachs and Susanne E. Ulbrich

    Citation: BMC Genomics 2019 20:679

    Content type: Research article

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  44. Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorder...

    Authors: Gabriel Costa Monteiro Moreira, Mayara Salvian, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Mônica Corrêa Ledur, Dorian Garrick, Gerson Barreto Mourão and Luiz L. Coutinho

    Citation: BMC Genomics 2019 20:669

    Content type: Research article

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  45. Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to...

    Authors: Farouk Messad, Isabelle Louveau, Basile Koffi, Hélène Gilbert and Florence Gondret

    Citation: BMC Genomics 2019 20:659

    Content type: Research article

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  46. Despite the convergence of rapid technological advances in genomics and the maturing field of ecoimmunology, our understanding of the genes that regulate immunity in wild populations is still nascent. Previous...

    Authors: Cassandra S. Scalf, Julia H. Chariker, Eric C. Rouchka and Noah T. Ashley

    Citation: BMC Genomics 2019 20:647

    Content type: Research article

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  47. Epigenetic changes such as cytosine (CpG) DNA methylations regulate gene expression patterns in response to environmental cues including infections. Microbial infections induce DNA methylations that play a pot...

    Authors: Basavaraj Sajjanar, Nares Trakooljul, Klaus Wimmers and Siriluck Ponsuksili

    Citation: BMC Genomics 2019 20:623

    Content type: Research article

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  48. The impossibility of closing the life cycle of the European eel (Anguilla anguilla) in captivity troubles the future of this critically endangered species. In addition, the European eel is a highly valued and dem...

    Authors: Christoffer Rozenfeld, Víctor García-Carpintero, Luz Pérez, Victor Gallego, Juan Germán Herranz-Jusdado, Helge Tveiten, Helge K. Johnsen, Romain Fontaine, Finn-Arne Weltzien, Joaquín Cañizares, Juan F. Asturiano and David S. Peñaranda

    Citation: BMC Genomics 2019 20:597

    Content type: Research article

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  49. Atrazine is widely used in agriculture and is a known endocrine disrupting chemical. Atrazine can seep into the water body through surface, posing a potential threat to the aquatic ecological environment and h...

    Authors: Fang Wang, Qian-wen Yang, Wen-Jie Zhao, Qi-Yan Du and Zhong-Jie Chang

    Citation: BMC Genomics 2019 20:587

    Content type: Research article

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  50. Egg quality can be defined as the egg ability to be fertilized and subsequently develop into a normal embryo. Previous research has shed light on factors that can influence egg quality. Large gaps however rema...

    Authors: Caroline T. Cheung, Thao-vi Nguyen, Aurélie Le Cam, Amélie Patinote, Laurent Journot, Christelle Reynes and Julien Bobe

    Citation: BMC Genomics 2019 20:584

    Content type: Research article

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