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. Research article

    Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

    Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty n...

    K. O. Skaftnesmo, R. B. Edvardsen, T. Furmanek, D. Crespo, E. Andersson, L. Kleppe, G. L. Taranger, J. Bogerd, R. W. Schulz and A. Wargelius

    BMC Genomics 2017 18:801

    Published on: 18 October 2017

  2. Research article

    Candidate lethal haplotypes and causal mutations in Angus cattle

    If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating ...

    Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel and Jeremy F. Taylor

    BMC Genomics 2017 18:799

    Published on: 18 October 2017

  3. Research article

    A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)

    The impact of nutritional status and diet composition on mitochondrial oxidative phosphorylation (OXPHOS) in fish remains largely unknown. To identify biomarkers of interest in nutritional studies, herein we o...

    Jonás I. Silva-Marrero, Alberto Sáez, Albert Caballero-Solares, Ivan Viegas, María Pilar Almajano, Felipe Fernández, Isabel V. Baanante and Isidoro Metón

    BMC Genomics 2017 18:768

    Published on: 11 October 2017

  4. Research article

    Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus)

    Cashmere growth is a seasonal and cyclic phenomenon under the control of photoperiod and multiple stimulatory and inhibitory signals. Beyond relevant coding genes, microRNA (miRNA) and long non coding RNA (lnc...

    Shanhe Wang, Wei Ge, Zhixin Luo, Yang Guo, Beilei Jiao, Lei Qu, Zhiying Zhang and Xin Wang

    BMC Genomics 2017 18:767

    Published on: 11 October 2017

  5. Research article

    Germline mutation within COL2A1 associated with lethal chondrodysplasia in a polled Holstein family

    The bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the...

    Sina Reinartz, Hartmut Mohwinkel, Christian Sürie, Maren Hellige, Karsten Feige, Deborah Eikelberg, Andreas Beineke, Julia Metzger and Ottmar Distl

    BMC Genomics 2017 18:762

    Published on: 10 October 2017

  6. Research article

    Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing

    Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide stu...

    Yanli Zhang, Fengzhe Li, Xu Feng, Hua Yang, Aoxiang Zhu, Jing Pang, Le Han, Tingting Zhang, Xiaolei Yao and Feng Wang

    BMC Genomics 2017 18:759

    Published on: 2 October 2017

  7. Research article

    Transcriptome analysis reveals differences in mechanisms regulating cessation of luteal function in pregnant and non-pregnant dogs

    In the domestic dog, corpora lutea (CL) are the only source of progesterone (P4), both in pregnant and non-pregnant cycles because there is no placental steroidogenesis. The absence of an endogenous luteolysin...

    Sophie Zatta, Hubert Rehrauer, Aykut Gram, Alois Boos and Mariusz Pawel Kowalewski

    BMC Genomics 2017 18:757

    Published on: 27 September 2017

  8. Research article

    Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae

    This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck’s ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangoli...

    Zelda du Toit, Morné du Plessis, Desiré L. Dalton, Raymond Jansen, J. Paul Grobler and Antoinette Kotzé

    BMC Genomics 2017 18:746

    Published on: 21 September 2017

  9. Research article

    Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup

    Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of...

    Robert Kammerer, Martin Mansfeld, Jana Hänske, Sophie Mißbach, Xiaocui He, Bernd Köllner, Susan Mouchantat and Wolfgang Zimmermann

    BMC Genomics 2017 18:717

    Published on: 11 September 2017

  10. Research article

    Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma

    Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbati...

    Laurence Tessier, Olivier Côté, Mary Ellen Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders and Dorothee Bienzle

    BMC Genomics 2017 18:708

    Published on: 8 September 2017

  11. Research article

    Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

    Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. There...

    Khalil Eslamloo, Xi Xue, Jennifer R. Hall, Nicole C. Smith, Albert Caballero-Solares, Christopher C. Parrish, Richard G. Taylor and Matthew L. Rise

    BMC Genomics 2017 18:706

    Published on: 8 September 2017

  12. Original Paper

    Genome-wide association study reveals putative role of gga-miR-15a in controlling feed conversion ratio in layer chickens

    Efficient use of feed resources for farm animals is a critical concern in animal husbandry. Numerous genetic and nutritional studies have been conducted to investigate feed efficiency during the regular laying...

    Jingwei Yuan, Sirui Chen, Fengying Shi, Guiqin Wu, Aiqiao Liu, Ning Yang and Congjiao Sun

    BMC Genomics 2017 18:699

    Published on: 6 September 2017

  13. Research article

    Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken

    The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for th...

    Julie A. Hicks, Tom E. Porter and Hsiao-Ching Liu

    BMC Genomics 2017 18:687

    Published on: 5 September 2017

  14. Research article

    A GJA9 frameshift variant is associated with polyneuropathy in Leonberger dogs

    Many inherited polyneuropathies (PN) observed in dogs have clinical similarities to the genetically heterogeneous group of Charcot-Marie-Tooth (CMT) peripheral neuropathies in humans. The canine disorders coll...

    Doreen Becker, Katie M. Minor, Anna Letko, Kari J. Ekenstedt, Vidhya Jagannathan, Tosso Leeb, G. Diane Shelton, James R. Mickelson and Cord Drögemüller

    BMC Genomics 2017 18:662

    Published on: 25 August 2017

  15. Research article

    MicroRNA expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli in vitro

    Coliform mastitis is a symptom of postpartum dysgalactia syndrome (PDS), a multifactorial infectious disease of sows. Our previous study showed gene expression profile change after bacterial challenge of porci...

    A. Jaeger, F. Hadlich, N. Kemper, A. Lübke-Becker, E. Muráni, K. Wimmers and S. Ponsuksili

    BMC Genomics 2017 18:660

    Published on: 24 August 2017

  16. Research article

    Comparing the intestinal transcriptome of Meishan and Large White piglets during late fetal development reveals genes involved in glucose and lipid metabolism and immunity as valuable clues of intestinal maturity

    Maturity of intestinal functions is critical for neonatal health and survival, but comprehensive description of mechanisms underlying intestinal maturation that occur during late gestation still remain poorly ...

    Ying Yao, Valentin Voillet, Maeva Jegou, Magali SanCristobal, Samir Dou, Véronique Romé, Yannick Lippi, Yvon Billon, Marie-Christine Père, Gaëlle Boudry, Laure Gress, Nathalie Iannucelli, Pierre Mormède, Hélène Quesnel, Laurianne Canario, Laurence Liaubet…

    BMC Genomics 2017 18:647

    Published on: 22 August 2017

  17. Research article

    Maternal nutrient restriction in mid-to-late gestation influences fetal mRNA expression in muscle tissues in beef cattle

    Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared ...

    Francois Paradis, Katie M. Wood, Kendall C. Swanson, Stephen P. Miller, Brian W. McBride and Carolyn Fitzsimmons

    BMC Genomics 2017 18:632

    Published on: 18 August 2017

  18. Research

    AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut

    The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs a...

    Kevin Cadwell, Sherko S. Niranji, Vanessa L. Armstrong, Catherine A. Mowbray, Richard Bailey, Kellie A Watson and Judith Hall

    BMC Genomics 2017 18:637

    Published on: 18 August 2017

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