Molecular Cytogenetics and Genomics Laboratory
Recent Publications
2012
Avila, F., Das, P.J., Kutzler, M., Owens, E., Perelman, P.,
Rubes, J., Johnson, W.E. and Raudsepp.T. 2012. Development and
application of molecular tools for camelid cytogenetics. The
Journal of Heredity (special issue for camelid genetics; accepted
for publication).
Avila, F., Das, P.J., Kutzler, M.A., Owens,
E., Perelman, P., Raudsepp, T. 2012. Development and
application of molecular tools for camelid cytogenetics.
Cytogenetics and Genome Research 136:314-359(11).
Das, P.J., Mishra, D. K., Avila, F., Johnson, G., Chowdhary, B.
P., Raudsepp, T. 2012. Identification and expression analysis of
the pig pseudoautosomal region using molecular cytogenetics
approach. Cytogenet Genome Res 136:314-359(13).
Ferrer, M., Anderson, D., Jones, M., Raudsepp, T., Avila, F.,
Miesner, M., DeBey, B., Kutzler, M. 2012. Segmental aplasia of the
right uterine horn with mucometra in an alpaca. JAVMA
241(6):697-700.
Janečka JE, Chowdhary B, Murphy WJ. 2012. Exploring the
correlations between sequence evolution rate and phenotypic
divergence across the Mammalian tree provides insights into
adaptive evolution. Journal of Bioscience 37:1-13.
Janečka JE. 2012. Tracks of my soul. In: Snow Leopard
Stories from the Roof of the World. Don Hunter, Editor.
University Colorado Press. Pp. 25-31
Holbrook JD, De Young RW, Janečka JE, Tewes ME, Honeycutt
RL, Young JH. 2012. Genetic diversity, population structure, and
movements of mountain lions (Puma concolor) in Texas. Journal of
Mammalogy 93:989-1000.
Murphy MJ, Janečka JE, Stadler T, Eizirik E, Ryder OA,
Gatesy J, Meredith RW, Springer MS. 2012. Response to Comment on
"Impacts of the Cretaceous Terrestrial Revolution and KPg
Extinction on Mammal Diversification". Science
337:34-35.
Raudsepp T, Das PJ, Avila F, Chowdhary BP. 2012. The
pseudoautosomal region and sex chromosome aneuploidies in domestic
species. Sex Development 6(1-3):72-83.
Rodgers T, JanečkaJE. 2012. Applications and techniques for
non-invasive faecal genetics research in felid conservation.
European Journal of Wildlife Research DOI:
10.1007/s10344-012-0675-6.
Rosen T, Hussain S, Mohammad G, Jackson R, Janečka JE,
Michel S. 2012. Reconciling sustainable development of mountain
communities with large carnivore conservation. Mountain Research
and Development 32:286-293.
Springer MS, Meredith R, Gatesy J, Emerling C, Park
J, Rabosky D, Stadler TC, Ryder O, JanečkaJE, Fisher C, Murphy W.
2012. Macroevolutionary dynamics and historical biogeography of
primate diversification inferred from a species supermatrix. PLoS
ONE 7:11:e49521:1-23.
Steelman SM, Chowdhary BP. 2012. Plasma
proteomics shows an elevation of the
anti-inflammatory protein APOA-IV in chronic equine laminitis. BMC
Vet Res. 8(179).
Steelman S, Chowdhary B, Suchodolski J, Dowd S, JanečkaJE. 2012.
Pyrosequencing of 16s rRNA Genes in fecal samples reveals high
diversity of hindgut microflora in horses and potential links to
chronic laminitis. BMC Veterinary Research 8:231. DOI:
10.1186/1746-6148-8-231
2011
Anwar MB, Jackson R, Nadeem MS, Janecka JE, S
Hussain, Beg MA, Ghulam M, and Qayyum M (2011) Food habits of snow
leopard Panthera uncia (Schreber, 1775) in Baltistan,
Northern Pakistan. European Journal of Wildlife
Research. 57:1077-1083.
Durkin K, Raudsepp T and
Chowdhary BP (2011) Cytogenetic Evaluation of the
Stallion. In Equine Reproduction. (Eds. A.O. McKinnon,
E.L. Squires, W.E. Vaala and D.D. Varner), Wiley Blackwell, Ch.
306.
Gilad O, Janecka, JE, Armstrong F, Tewes ME,
Honeycutt TL (2011) Mountain lions in Guadalupe Mountains National
Park: Estimates of occurrence and distribution through DNA
analysis. Southwestern Association of Naturalists.
56:297-304.
Janecka JE, Munkhtsog B, Jackson RM, Mallon DP,
Naranbaatar G, Gerelmaa K, Murphy WJ (2011) Comparison of
noninvasive genetic and camera-trapping techniques for surveying
snow leopards. Journal of Mammalogy.92:771-783.
Janečka JE, Tewes ME, Laack LL, Caso A, Grassman LI
Jr, Haines AM, Shindle D, Davis B, Murphy WJ, Honeycutt RL (2011)
Reduced genetic diversity and isolation of remnant ocelot
populations occupying a severely fragmented landscape in southern
Texas. Animal Conservation. 14:608-619.
Kachroo, P., Ivanov, I., Davidson, L.A.,
Chowdhary, B.P., Lupton, J.R., Chapkin, R.S. 2011.
Classification of Diet-Modulated Gene Signatures at the Colon
Cancer Initiation and Progression Stages. Digestive Diseases
and Sciences. 9:2595-604.
Li G, Janecka JE, Murphy WJ (2011) Accelerated
evolution of a putative premating isolation gene,
CES7, in the cat family. Molecular Biology and
Evolution. 28:911-920.
*Meredith, RW,
*Janečka JE, Gatesy J, Ryder OA, Fisher CA,
Teeling EC, Alisha Goodbla A, Eizirik E, Simão TLL, Stadler T,
Rabosky DL, Honeycutt RL, Flynn JF, Ingram CI, Steiner C, Williams
TL, Robinson TJR, Burk-Herrick A, Westerman M, Ayoub NA, *Springer
MS, *Murphy WJ (2011) Impacts of the Cretaceous Terrestrial
Revolution and KPg Extinction on Extant Mammal Diversification.
Science 334:521-524.*These authros contributed
equally.
Paria,
N.*, Raudsepp, T* ., Wilkerson, A.J., O'Brien,
P.C.M., Ferguson-Smith, M.A., Love, C.C., Arnold, C., Rakestraw,
P., Murphy, W.J., Chowdhary, B.P. (2011) A gene
catalogue of the euchromatic male specific region of the horse Y
chromosome: Comparison with human and other mammals. PLoS ONE
6(7):e212374: 1-13. *These authors have equal
contribution
Raudsepp, T. and Chowdhary, B.P. 2011.
Cytogenetics and physical chromosome maps. Chpt. 7. In: The
Genetics of the Pig (Eds. A. Ruvinsky and M. Rothschild),
CAB International, pp. 134-78.
Springer MS, Meredith RW, Janecka JE, Murphy WJ
(2011) The historical biogeography of Mammalia. Jones
KE and Safi K (eds) Global Biodiversity of Mammals: Past, Present
and Future. Philosophical Transactions of the Royal Society
B: Biological Sciences (Invited Paper for Special
Issue). 366:2478-2502.
2010
Das, P.J., Paria, N.,
Gustafson-Seabury, A., Vishnoi, M., Chaki, S., Love,
C.C., Varner, D.D., Chowdhary, B.P.,
Raudsepp, T. 2010. Total RNA isolation from stallion
sperm and testis biopsies. Theriogenology, 74,
1099-1106
Das, P.J., Vishnoi, M., Kachroo, P.,
Wang, J., Love, C.C., Varner, D.D.,
Chowdhary, B.P., Raudsepp, T. 2010.
Expression microarray profiling of sperm and testis mRNA of
reproductively normal stallions. Animal Reproduction
Science, 121S, S175.
Juras R., Raudsepp T., Das P.J.,
Conant E., Cothran E.G. 2010. XX/XY blood lymphocyte chimerism in
heterosexual dizygotic American Bashkir Curly horse twins. J
Equine Vet Sci 30, 575-580.
Raudsepp, T. , Durkin, K., Lear, T.,
Das, P.J., Avila, F. Kachroo, P.,
Chowdhary, B.P. 2010. Molecular heterogeneity of XY
sex reversal in the horse. Animal
Genetics 41 (Suppl. 2), 41-52 (Special Issue on Horse
Genetics and Genomics).
Sudderth, A.K., Das, P.J., Varner, D.D., T.
Raudsepp, T. 2010. Determination of optimal semen
processing methods for total RNA isolation and sperm genomic
analysis. Animal Reproduction Science, 121S,
S149-S150.
2009
Alizadeh, A., Hong, L.Z, Kaelin, C.B, Raudsepp, T,
Manuel, H and Barsh, G.S. 2009. Genetics of Sex-linked
yellow in the Syrian hamster. Genetics,
181(4):1427-1436.
Brinkmeyer-Langford, CL, Childers C. Fritz K. Gustafson-
Seabury A. Cothran M. Raudsepp, T. Womack, JE
and Skow, LC. 2009. A High Resolution RH Map of the Bovine Major
Histocompatibility Complex. BMC Genomics,
10:182-191.
Bright LA, Burgess SC, Chowdhary BP, Swiderski CE,
McCarthy FM. Structural and functional-annotation of an equine
whole genome oligoarray. BMC Bioinformatics 2009;10:
1-8.
Das, P.J., Chowdhary, B.P.,
Raudsepp, T. 2009. Characterization of the bovine
pseudoautosomal region (PAR) and comparison with sheep, goat and
other mammalian PARs. Cytogenet. Genome
Res., 126, 139-147.
Davis BW, Raudsepp T, Pearks Wilkerson AJ, Agarwala
R, Schäffer AA, Houck M, Ryder OA, Chowdhdary BP,
Murphy WJ. 2009. A high-resolution cat radiation hybrid and
integrated FISH mapping resource for phylogenomic studies across
Felidae. Genomics, 93:299-304.
Di Meo GP, Perucatti A, Peretti V, Incarnato D, Ciotola F,
Liotta L, Raudsepp T, Di Berardino D,
Chowdhary B, Iannuzzi L. 2009. The 450-band resolution
G- and R-banded standard karyotype of the donkey (Equus
asinus, 2n = 62). Cytogenet Genome Res. 125:
266-271.
Liu J, Westhusin M, Johnson G, Raudsepp T,
Chowdhary B, Burghardt R, Long C, Kraemer D. 2009.
Evaluation of culture systems for attachment and proliferation of
the epithelial cells cultured from ovine semen. Anim Reprod
Sci. 115: 49-57.
Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A,
Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert
MTP, Dalén L, Arsuaga JL, Ericson PGP, Huson DH, Helgen KM, Murphy
WJ, Götherström A, Schuster SC (2009) The mitochondrial genome
sequence of the Tasmanian tiger (Thylacinus
cynocephalus). Genome Research 19:213-220.
Received JOURNAL COVER.
Schneider, D.A, Tibary, A., Raudsepp, T.,
Das, P.J., O'Rourke, K.I. 2009. Blood chimerism
confounds genetic relative susceptibility testing for classical
scrapie in sheep. J.Vet. Diagnostic Investigation,
21:295-305.
Shields, J.E., K.J. Kochan, K.J., Jeong, J., Abbey, C.A.,
Raudsepp, T., Riggs, P.K. 2009. Initial
characterization of a gene abundantly expressed in stallion testis.
J. Equine Vet. Sci., 29, 324-325
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F,
Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O,
Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MCT,
Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T,
Binns MM, Chowdhary BP, Coleman SJ, Della Valle G,
Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A,
Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG,
Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M,
Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC,
Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Broad Institute
Genome Sequencing Platfor, Broad Institute Whole Genome Assembly
Team, Lander ES, and Lindblad-Toh K. 2009. Genome sequence,
comparative analysis and population genetics of the domestic horse
(Equus caballus). Science 326 (5954):
865-867.
2008
Brinkmeyer-Langford C, Raudsepp T,
Gustafson-Seabury A, Chowdhary BP. 2008.
A BAC contig map over the proximal approximately 3.3 Mb region of
horse chromosome 21. Cytogenet. Genome Res.
120:164-172.
Chowdhary, B.P., Paria, N.P.,
Raudsepp, T. 2008. Potential applications of equine
genomics in dissecting diseases and fertility. Animal
Reproduction Science, 107, 208-218.
Chowdhary BP, Raudsepp T. 2008. The
Horse Genome Derby: racing from map to whole genome sequence.
Chromosome Res. 16, 109-127.
Janecka JE, Tewes ME, Laack LL, Grassman LI Jr,
Haines AM, Honeycutt RL (2008) Small effective population sizes of
two remnant ocelot populations (Leopardus pardalis
albescens) in the United States. Conservation
Genetics 9:869-878.
Janecka JE, Miller KM, Lim NT-L, Baba M, Izawa M,
Boeadi, Murphy WJ (2008) Evidence for multiple species of Sunda
colugos. Current Biology 18:R1001-R1002.
Janecka JE, Jackson R, Zhang Y, Li D, Munkhtsog B,
Buckley-Beason V, Murphy WJ (2008) Population monitoring of snow
leopards using noninvasive collection of scat samples: A pilot
study. Animal Conservation 11:401-411. Received
JOURNAL COVER.
Pearks-Wilkerson, A.J., Raudsepp, T., Graves, T.,
Warren, W., Chowdhary, B.P., Skow, L.C., Murphy, W.J.
2008. Physical mapping, gene discovery, and comparative analysis of
X-degenerate genes from the domestic cat Y chromosome. Genomics,
92: 329-338.
Raudsepp, T. and Chowdhary, B.P. 2008.
FISH for mapping single copy genes. In: Phylogenomics:
Methods in Molecular Biology (Ed. W. Murphy), Humana Press,
New Jersey, USA, pp.31-49.
Raudsepp, T. and Chowdhary, B. P.
2008. The horse pseudoautosomal region (PAR): characterization and
comparison with the human, chimp and mouse PARs. Cytogenet.
Genome Res. 121, 102-109.
Raudsepp, T., Gustafson-Seabury, A.,
Durkin, K., Wagner, M.L., Goh, G., Seabury, C.M.,
Brinkmeyer-Langford, C., Lee, E.-J., Agarwala, R., Stallknecht
Rice, E., Schäffer, A.A., Skow, L.C., Tozaki, T., Yasue, H., M.
Penedo, C.M., Lyons, L.A., Khazanehdari, K.A., Binns, M.M.,
MacLeod, J.N., Distl, O., Guérin, G., Leeb, T., Mickelson, J.R.,
Chowdhary, B.P. 2008. A 4103 marker integrated
physical and comparative map of the horse genome, Cytogenet.
Genome Res., 122, 28-36.
2007
Chiang, H.-I., Zhou, H., Raudsepp, T., Jesudhasan,
P.R., Zhu, J.J. 2007. Chicken CD69 and CD94/NKG2-like genes in a
chromosomal region syntenic to mammalian natural killer gene
complex. Immunogenetics 59, 603-611.
Coleman SJ, Gong G, Gaile DP,
Chowdhary BP, Bailey E, Liu L, MacLeod JN
(2007) Evaluation of Compass as a comparative mapping tool for ESTs
using horse radiation hybrid maps. Anim Genet
38:294-302
Goh, G*, Raudsepp, T*,
Durkin, K, Wagner, ML, Schäffer, AA, Agarwala, R,
Tozaki, T, Mickelson, JR and Chowdhary, BP. 2007.
High-resolution gene maps of horse chromosomes 14 and 21:
additional insights into evolution and rearrangements of HSA5
homologues in mammals. Genomics 89:89-112.
Received JOURNAL COVER, *equal
contribution.
Hansen GR, Abbey CA, Gaile DP, Raudsepp T,
Chowdhary BP, Womack JE, Gill CA. 2007. Assignment of
six genes to bovine chromosomes 5 and 16 by fluorescence in situ
hybridization, radiation hybrid mapping and genetic linkage
analysis. Cytogenet. Genome Res. 116: 194-197.
Herszberg B, Mata X, Giulotto E, Decaunes P,
Piras FM, Chowdhary BP, Chaffaux S, Guerin G (2007)
Characterization of the equine glycogen debranching enzyme gene
(AGL): Genomic and cDNA structure, localization, polymorphism and
expression. Gene 404:1-9
Janecka JE, Walker CW, Tewes ME, Caso A, Laack LL,
Honeycutt RL (2007) Phylogenetic relationships of ocelot
(Leopardus paradalis albescens) populations from the
Tamaulipan Biotic Province and implications for recovery.
Southwestern Naturalist 52:89-96. Received
JOURNAL COVER.
Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann
A, Helgen KM, Springer MS, Murphy WJ (2007) Molecular and genomic
data identify the closest living relative of primates.
Science 318:792-795.
Janecka JE, Grassman LI Jr, Honeycutt RL, Tewes ME
(2007) Whole genome amplification for sequencing and applications
in conservation genetics. The Journal of Wildlife
Management 71:1357-1360.
Janecka JE, Blankenship TL, Hirth DH, Kilpatrick
CW, Tewes ME, Grassman LI Jr (2007) Evidence for male-biased
dispersal in bobcats Lynx rufus using relatedness
analysis. Wildlife Biology 13:38-47.
Momozawa, Y., Takeuchi, Y.,Tozaki, T., Kikusui, T.,Hasegawa, T.,
Raudsepp, T., Chowdhary, B.P., Kusunose,
R. and Mori, Y. 2007. SNP detection and radiation hybrid mapping
horses of nine candidate genes for temperament. Animal Genetics,
38, 81-91.
Prause A, Guionaud CT, Klukowska-Rotzler J,
Giulotto E, Magnani E, Chowdhary BP, Philipp U, Leeb
T, Mevissen M (2007) Chromosomal assignment of five equine HTR
genes by FISH and RH mapping. Anim Genet
38:83-4.
Stübs D, Kuiper H, Mömke S, Chowdhary
BP, Distl O (2007) Assignment of the TYK2 gene to equine
chromosome 7q12-q13. Archiv für Tierzucht
50:322-323.