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

    Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping

    Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some t...

    Tingting Wang, Yi-Ping Phoebe Chen, Iona M. MacLeod, Jennie E. Pryce, Michael E. Goddard and Ben J. Hayes

    BMC Genomics 2017 18:618

    Published on: 15 August 2017

  2. Methodology article

    A phased SNP-based classification of sickle cell anemia HBB haplotypes

    Sickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. As HbF is the major modul...

    Elmutaz M. Shaikho, John J. Farrell, Abdulrahman Alsultan, Hatem Qutub, Amein K. Al-Ali, Maria Stella Figueiredo, David H.K. Chui, Lindsay A. Farrer, George J. Murphy, Gustavo Mostoslavsky, Paola Sebastiani and Martin H. Steinberg

    BMC Genomics 2017 18:608

    Published on: 11 August 2017

  3. Research article

    Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family

    Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addi...

    Yanxia Sun, Michael J. Moore, Nan Lin, Kole F. Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Jianqiang Li and Hengchang Wang

    BMC Genomics 2017 18:592

    Published on: 9 August 2017

  4. Research article

    Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

    Studying genetic variation distribution in proteins containing charged regions, called charge clusters (CCs), is of great interest to unravel their functional role. Charge clusters are 20 to 75 residue segment...

    Sabrine Belmabrouk, Najla Kharrat, Rania Abdelhedi, Amine Ben Ayed, Riadh Benmarzoug and Ahmed Rebai

    BMC Genomics 2017 18:588

    Published on: 8 August 2017

  5. Research article

    Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

    Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic ...

    Gabriele Andrea Lugli, Christian Milani, Francesca Turroni, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Chiara Ferrario, Monica Modesto, Paola Mattarelli, Killer Jiří, Douwe van Sinderen and Marco Ventura

    BMC Genomics 2017 18:568

    Published on: 1 August 2017

  6. Software

    COGNATE: comparative gene annotation characterizer

    The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization...

    Jeanne Wilbrandt, Bernhard Misof and Oliver Niehuis

    BMC Genomics 2017 18:535

    Published on: 17 July 2017

  7. Research article

    The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

    An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assemble...

    Shyam Gopalakrishnan, Jose A. Samaniego Castruita, Mikkel-Holger S. Sinding, Lukas F. K. Kuderna, Jannikke Räikkönen, Bent Petersen, Thomas Sicheritz-Ponten, Greger Larson, Ludovic Orlando, Tomas Marques-Bonet, Anders J. Hansen, Love Dalén and M. Thomas P. Gilbert

    BMC Genomics 2017 18:495

    Published on: 29 June 2017

  8. Research article

    Diversity and evolution of mariner-like elements in aphid genomes

    Although transposons have been identified in almost all organisms, genome-wide information on mariner elements in Aphididae remains unknown. Genomes of Acyrthosiphon pisum, Diuraphis noxia and Myzus persicae belo...

    Maryem Bouallègue, Jonathan Filée, Imen Kharrat, Maha Mezghani-Khemakhem, Jacques-Deric Rouault, Mohamed Makni and Pierre Capy

    BMC Genomics 2017 18:494

    Published on: 29 June 2017

  9. Editorial

    Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

    We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in th...

    Daniel J. Macqueen, Craig R. Primmer, Ross D. Houston, Barbara F. Nowak, Louis Bernatchez, Steinar Bergseth, William S. Davidson, Cristian Gallardo-Escárate, Tom Goldammer, Yann Guiguen, Patricia Iturra, James W. Kijas, Ben F. Koop, Sigbjørn Lien, Alejandro Maass, Samuel A. M. Martin…

    BMC Genomics 2017 18:484

    Published on: 27 June 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

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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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