Comparative and evolutionary genomics

Section edited by Igor Rogozin

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

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  1. Research article

    100 million years of multigene family evolution: origin and evolution of the avian MHC class IIB

    Gene duplication has led to a most remarkable adaptation involved in vertebrates’ host-pathogen arms-race, the major histocompatibility complex (MHC). However, MHC duplication history is as yet poorly understo...

    Julien Goebel, Marta Promerová, Francesco Bonadonna, Karen D. McCoy, Céline Serbielle, Maria Strandh, Glenn Yannic, Reto Burri and Luca Fumagalli

    BMC Genomics 2017 18:460

    Published on: 13 June 2017

  2. Research article

    Intricacies in arrangement of SNP haplotypes suggest “Great Admixture” that created modern humans

    Inferring history from genomic sequences is challenging and problematic because chromosomes are mosaics of thousands of small Identicalby-descent (IBD) fragments, each of them having their own unique story. Ho...

    Rajib Dutta, Joseph Mainsah, Yuriy Yatskiv, Sharmistha Chakrabortty, Patrick Brennan, Basil Khuder, Shuhao Qiu, Larisa Fedorova and Alexei Fedorov

    BMC Genomics 2017 18:433

    Published on: 5 June 2017

  3. Research article

    Gene expression and adaptive noncoding changes during human evolution

    Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive c...

    Courtney C. Babbitt, Ralph Haygood, William J. Nielsen and Gregory A. Wray

    BMC Genomics 2017 18:435

    Published on: 5 June 2017

  4. Research article

    The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes

    Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the pr...

    Shara Atambayeva, Raigul Niyazova, Anatoliy Ivashchenko, Anna Pyrkova, Ilya Pinsky, Aigul Akimniyazova and Siegfried Labeit

    BMC Genomics 2017 18:428

    Published on: 1 June 2017

  5. Research article

    Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

    Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFIT...

    Irene Bassano, Swee Hoe Ong, Nathan Lawless, Thomas Whitehead, Mark Fife and Paul Kellam

    BMC Genomics 2017 18:419

    Published on: 30 May 2017

  6. Research article

    Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi

    Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and num...

    G. Margos, S. Hepner, C. Mang, D. Marosevic, S. E. Reynolds, S. Krebs, A. Sing, M. Derdakova, M. A. Reiter and V. Fingerle

    BMC Genomics 2017 18:422

    Published on: 30 May 2017

  7. Research article

    Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

    Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics be...

    J. B. Butler, R. E. Vaillancourt, B. M. Potts, D. J. Lee, G. J. King, A. Baten, M. Shepherd and J. S. Freeman

    BMC Genomics 2017 18:397

    Published on: 22 May 2017

  8. Research article

    Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues

    Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both col...

    Lauren E. Des Marteaux, Alexander H McKinnon, Hiroko Udaka, Jantina Toxopeus and Brent J. Sinclair

    BMC Genomics 2017 18:357

    Published on: 8 May 2017

  9. Research article

    Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages

    Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in whic...

    Deyvid Amgarten, Layla Farage Martins, Karen Cristina Lombardi, Luciana Principal Antunes, Ana Paula Silva de Souza, Gianlucca Gonçalves Nicastro, Elliott Watanabe Kitajima, Ronaldo Bento Quaggio, Chris Upton, João Carlos Setubal and Aline Maria da Silva

    BMC Genomics 2017 18:346

    Published on: 4 May 2017

  10. Research article

    Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python

    Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process....

    Audra L. Andrew, Blair W. Perry, Daren C. Card, Drew R. Schield, Robert P. Ruggiero, Suzanne E. McGaugh, Amit Choudhary, Stephen M. Secor and Todd A. Castoe

    BMC Genomics 2017 18:338

    Published on: 2 May 2017

  11. Research article

    Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates

    Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates.

    Lucie Marandel, Stéphane Panserat, Elisabeth Plagnes-Juan, Eva Arbenoits, José Luis Soengas and Julien Bobe

    BMC Genomics 2017 18:342

    Published on: 2 May 2017

  12. Software

    CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

    The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuit...

    Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar and W. Florian Fricke

    BMC Genomics 2017 18:332

    Published on: 27 April 2017

  13. Methodology article

    A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

    Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material.

    Tran Thi Ngoc Dung, Pham Thanh Duy, October M. Sessions, Uma K. Sangumathi, Voong Vinh Phat, Pham Thi Thanh Tam, Nguyen Thi Nguyen To, Tran My Phuc, Tran Thi Hong Chau, Nguyen Ngoc Minh Chau, Ngoc Nguyen Minh, Guy E. Thwaites, Maia A. Rabaa and Stephen Baker

    BMC Genomics 2017 18:324

    Published on: 24 April 2017

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Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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