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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.

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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. The synthetic 17α-ethinylestradiol (EE2) is a common estrogenic pollutant that has been suspected to affect the demography of river-dwelling salmonids. One possibility is that exposure to EE2 tips the balance ...

    Authors: Oliver M. Selmoni, Diane Maitre, Julien Roux, Laetitia G. E. Wilkins, Lucas Marques da Cunha, Etienne L. M. Vermeirssen, Susanne Knörr, Marc Robinson-Rechavi and Claus Wedekind

    Citation: BMC Genomics 2019 20:583

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:371

  35. Subfertility is one challenge facing the dairy industry as the average Holstein heifer conception rate (HCR), the proportion of heifers that conceive and maintain a pregnancy per breeding, is estimated at 55–6...

    Authors: Jennifer N. Kiser, Elizabeth M. Keuter, Christopher M. Seabury, Mahesh Neupane, Joao G. N. Moraes, Joseph Dalton, Gregory W. Burns, Thomas E. Spencer and Holly L. Neibergs

    Citation: BMC Genomics 2019 20:576

    Content type: Research article

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  36. The production of foam nests is one of the strategies that has evolved to allow some anuran species to protect their eggs and larvae. Despite considerable knowledge of the biochemical components of and constru...

    Authors: Wei Zhang, Li Huang, Jun Li, Yinghua Li, Shichao Wei, Ling Cai and Hua Wu

    Citation: BMC Genomics 2019 20:562

    Content type: Research article

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  37. National genetic evaluations for disease resistance do not exist, precluding the genetic improvement of cattle for these traits. We imputed BovineHD genotypes to whole genome sequence for 2703 Holsteins that w...

    Authors: Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel, Christopher M. Seabury, Holly L. Neibergs and Jeremy F. Taylor

    Citation: BMC Genomics 2019 20:555

    Content type: Research article

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  38. The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an ...

    Authors: Anja Striberny, Even H. Jørgensen, Christophe Klopp and Elodie Magnanou

    Citation: BMC Genomics 2019 20:529

    Content type: Research article

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  39. Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar prod...

    Authors: Marc G. Higgins, David A. Kenny, Claire Fitzsimons, Gordon Blackshields, Séan Coyle, Clare McKenna, Mark McGee, Derek W. Morris and Sinéad M. Waters

    Citation: BMC Genomics 2019 20:525

    Content type: Research article

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  40. The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we...

    Authors: Rayner González-Prendes, Emilio Mármol-Sánchez, Raquel Quintanilla, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Tainã Figueiredo Cardoso, Arianna Manunza, Ángela Cánovas and Marcel Amills

    Citation: BMC Genomics 2019 20:518

    Content type: Research article

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  41. Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish s...

    Authors: Mingkun Luo, Lanmei Wang, Haoran Yin, Wenbin Zhu, Jianjun Fu and Zaijie Dong

    Citation: BMC Genomics 2019 20:515

    Content type: Research article

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  42. Dermal papilla cells (DPCs), the “signaling center” of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in...

    Authors: Sen Ma, Ying Wang, Guangxian Zhou, Yi Ding, Yuxin Yang, Xiaolong Wang, Enping Zhang and Yulin Chen

    Citation: BMC Genomics 2019 20:512

    Content type: Research article

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  43. In female mammals, the initiation of puberty, coupling with the dramatically morphological changes in ovaries, indicates the sexual and follicular maturation. Previous studies have suggested that the disrupted...

    Authors: Xiaolong Yuan, Shaopan Ye, Zitao Chen, Xiangchun Pan, Shuwen Huang, Zhonghui Li, Yuyi Zhong, Ning Gao, Hao Zhang, Jiaqi Li and Zhe Zhang

    Citation: BMC Genomics 2019 20:510

    Content type: Research article

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  44. Livestock production aims to provide meats of high and consistent eating quality. Insufficient intramuscular (IM) fat and excessive subcutaneous (SC) fat are paramount pork quality challenges. IM fat and SC fa...

    Authors: Wenjing Wu, Dawei Zhang, Yajun Yin, Miao Ji, Ke Xu, Xin Huang, Yongjia Peng and Jin Zhang

    Citation: BMC Genomics 2019 20:509

    Content type: Research article

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  45. We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress i...

    Authors: Allen H. Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh and Carl Schmidt

    Citation: BMC Genomics 2019 20:502

    Content type: Research article

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  46. Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.

    Authors: Lingyang Xu, Liu Yang, Bo Zhu, Wengang Zhang, Zezhao Wang, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, George E. Liu and Junya Li

    Citation: BMC Genomics 2019 20:494

    Content type: Research article

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  47. Epigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in...

    Authors: Siriluck Ponsuksili, Nares Trakooljul, Sajjanar Basavaraj, Frieder Hadlich, Eduard Murani and Klaus Wimmers

    Citation: BMC Genomics 2019 20:492

    Content type: Research article

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