Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals

Janine Deakin, Edda Koina, Paul Waters, Ruth Doherty, V Patel, Margaret Delbridge, Bianca Dobson, James Fong, Yanqiu Hu, Cecilia van den Hurk, Andrew Pask, Geoff Shaw, Carly Smith, Katherine Thompson, Matthew Wakefield, Hongshi Yu, Marilyn Renfree, Jennifer Marshall Graves

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two hromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and Fneo-X_ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.
Original languageEnglish
Pages (from-to)1159-1175
Number of pages17
JournalChromosome Research
Volume16
DOIs
Publication statusPublished - 2008
Externally publishedYes

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Chromosomes, Human, 1-3
Macropodidae
Marsupialia
Mammals
Opossums
Chromosomes
Synteny
Chromosomes, Human, Pair 5
Cytogenetics
Monodelphis
Chromosomes, Human, X
Genome
Internal-External Control
Chromosome Mapping
X Chromosome
Gene Silencing
Genes

Cite this

Deakin, J., Koina, E., Waters, P., Doherty, R., Patel, V., Delbridge, M., ... Marshall Graves, J. (2008). Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals. Chromosome Research, 16, 1159-1175. https://doi.org/10.1007/s10577-008-1266-y
Deakin, Janine ; Koina, Edda ; Waters, Paul ; Doherty, Ruth ; Patel, V ; Delbridge, Margaret ; Dobson, Bianca ; Fong, James ; Hu, Yanqiu ; van den Hurk, Cecilia ; Pask, Andrew ; Shaw, Geoff ; Smith, Carly ; Thompson, Katherine ; Wakefield, Matthew ; Yu, Hongshi ; Renfree, Marilyn ; Marshall Graves, Jennifer. / Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals. In: Chromosome Research. 2008 ; Vol. 16. pp. 1159-1175.
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abstract = "Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two hromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and Fneo-X_ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.",
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Deakin, J, Koina, E, Waters, P, Doherty, R, Patel, V, Delbridge, M, Dobson, B, Fong, J, Hu, Y, van den Hurk, C, Pask, A, Shaw, G, Smith, C, Thompson, K, Wakefield, M, Yu, H, Renfree, M & Marshall Graves, J 2008, 'Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals', Chromosome Research, vol. 16, pp. 1159-1175. https://doi.org/10.1007/s10577-008-1266-y

Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals. / Deakin, Janine; Koina, Edda; Waters, Paul; Doherty, Ruth; Patel, V; Delbridge, Margaret; Dobson, Bianca; Fong, James; Hu, Yanqiu; van den Hurk, Cecilia; Pask, Andrew; Shaw, Geoff; Smith, Carly; Thompson, Katherine; Wakefield, Matthew; Yu, Hongshi; Renfree, Marilyn; Marshall Graves, Jennifer.

In: Chromosome Research, Vol. 16, 2008, p. 1159-1175.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals

AU - Deakin, Janine

AU - Koina, Edda

AU - Waters, Paul

AU - Doherty, Ruth

AU - Patel, V

AU - Delbridge, Margaret

AU - Dobson, Bianca

AU - Fong, James

AU - Hu, Yanqiu

AU - van den Hurk, Cecilia

AU - Pask, Andrew

AU - Shaw, Geoff

AU - Smith, Carly

AU - Thompson, Katherine

AU - Wakefield, Matthew

AU - Yu, Hongshi

AU - Renfree, Marilyn

AU - Marshall Graves, Jennifer

PY - 2008

Y1 - 2008

N2 - Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two hromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and Fneo-X_ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.

AB - Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two hromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and Fneo-X_ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.

U2 - 10.1007/s10577-008-1266-y

DO - 10.1007/s10577-008-1266-y

M3 - Article

VL - 16

SP - 1159

EP - 1175

JO - Chromosome Research

JF - Chromosome Research

SN - 0967-3849

ER -