TY - JOUR
T1 - Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha
AU - Hardin, Aaron
AU - Nevonen, Kimberly A.
AU - Eckalbar, Walter L.
AU - Carbone, Lucia
AU - Ahituv, Nadav
N1 - Funding Information:
We thank Irvin Modlin and Mark Kidd (Yale University) for providing M. coucha from their colony, David Safronetz (Rocky Mountain Laboratories) for Mastomys advice, Jeff Wall (UCSF) for assistance with the genome assembly, Leigh Richards and the Durban Natural Science Museum for wild Mastomys samples, Nicola Illing and Mandy Mason (University of Cape Town) for extracting DNA from these samples, and Katie Pollard (Gladstone Institute and UCSF) for advice with comparative genomics. This work was supported in part by the National Human Genome Research Institute (NHGRI) grant number 1R01HG010333 (for N.A. and L.C.). L.C. is supported in part by the NIH Office of the Director, NIH/OD P51 OD011092 and the National Science Foundation (grant 1613856). N.A. is supported in part by the National Human Genome Research Institute 1UM1HG009408, National Institute of Mental Health grant numbers 1R01MH109907 and 1U01MH116438, National Institute of Child & Human Development 1P01HD084387, National Institute of Diabetes and Digestive and Kidney Diseases 1R01DK116738, and National Heart Lung and Blood Institute 1R01HL138424.
Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.
AB - Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.
KW - Comparative genomics
KW - Mastomys
KW - mammary glands
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U2 - 10.1093/molbev/msz188
DO - 10.1093/molbev/msz188
M3 - Article
C2 - 31424545
AN - SCOPUS:85075813973
SN - 0737-4038
VL - 36
SP - 2805
EP - 2812
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 12
ER -