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Wong, Emily; Young, Lauren J.; Papenfuss, Anthony T.; Belov, Katherine

doi:10.1186/1745-7580-2-4

Cited by 41 publications

(18 citation statements)

References 54 publications

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“…Many immune genes are likely to be left unannotated by automated annotation pipelines, such as Ensembl, due to their more rapid evolution. To increase the sensitivity of immune gene identification we used manually curated opossum ( Monodelphis domestica ) immune gene lists [ 36 , 37 ] of 1,549 opossum genes. Less than a third (463) of these were annotated by the Ensembl opossum geneset.…”

Section: Resultsmentioning

confidence: 99%

“…We considered reads that align with less than 5% of the sequence to an exon to be intergenic. Curated immune gene lists derived from Belov et al 2007 [ 36 ] and Wong et al 2006 [ 37 ] were specially used to derive read counts for immune genes. Fisher's exact test was used to test for differential expression between the two thymuses using the R statistical language [ 121 ].…”

Section: Methodsmentioning

confidence: 99%

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Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

et al. 2011

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BackgroundThe thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby.ResultsWe show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed.ConclusionThis is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

et al. 2011

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“…Studies of the broader immune system have revealed high levels of innovation through expansions of many other immune-related gene families in the opossum, indicating possible specializations to the metatherian variant of mammalian life. For example, Belov and colleagues (Wong et al 2006;Belov et al 2007) employed a combination of semiautomated and manual curation strategies to discover and describe the genomic organization of rapidly evolving immunerelated families, many of whose members which went undetected in the initial genome annotation. These include: chemokines, cytokines, cytokine receptors, natural killer cell receptors, leukocyte receptors, natural killer-associated Ig-like receptors, and members of the wide-spectrum antimicrobial cathelicidin and defensin families.…”

Section: Immunogeneticsmentioning

confidence: 99%

The opossum genome: Insights and opportunities from an alternative mammal

Samollow¹

2008

Genome Res.

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The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.Compilation and publication of the genome sequence of the gray short-tailed opossum, Monodelphis domestica, a metatherian (marsupial) mammal (Mikkelsen et al. 2007b), create unique opportunities for investigating the evolutionary processes that have shaped the structural and functional attributes of mammalian and other vertebrate genomes. These opportunities arise from both the unique phylogenetic position of metatherians in the vertebrate scheme and some fundamental characteristics of metatherians that distinguish them from other mammalian species.Modern mammals comprise three major lineages (Fig. 1). Judged from multiple nuclear sequence and mtDNA alignments, the most closely related of these, the Metatheria and Eutheria (placental mammals), diverged from their most recent common ancestor ∼173-190 million years ago (Mya) (Kumar and Hedges 1998;Woodburne et al. 2003;van Rheede et al. 2006). The other major clade, the Prototheria, of which the egg-laying monotremes (platypus and four species of echidnas) are the only living representatives, branched off 20-35 million years (Myr) prior to the metatherian-eutherian divergence (Phillips and Penny 2003;Woodburne et al. 2003;van Rheede et al. 2006). 2 By way of reference, the separation of mammals and birds occurred at least 310 Mya (d...

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“…These are important steps for developing marsupial T-cell markers. (19) In one of the companion papers to the opossum genome paper, Belov and colleagues (4) identified all the immune genes in a marsupial, including chemokines, defensins, cathelicidins, and NK receptors. Not surprisingly (despite earlier speculations to the contrary), marsupials have the same immune gene complement and gene clusters as in eutherians.…”

Section: The Opossum Immunomementioning

confidence: 99%

The genome of a Gondwanan mammal

Renfree

2007

BioEssays

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Australia is thought of as the home of marsupials, but South America has 60 or so species of these interesting mammals. The genome of one of these, the South American grey short-tailed opossum, Monodelphis domestica, has just been sequenced and published in June.1 The high quality 6x coverage is the first marsupial genome completed, pipping the 2x coverage of the Australian tammar wallaby at the post by half a year. The opossum genome has an unusual structure with fewer chromosomes than the human genome (9 pairs versus 23 pairs) but a longer total length (3.4 billion versus 3 billion bases). The opossum autosomes, like those of all marsupials, are extremely large but, in contrast, the X chromosome is only 76 Mb long. The opossum genome has turned up several surprises and provided critical new information on the evolution of mammalian genomes.

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Cited by 41 publications

References 54 publications

Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

The opossum genome: Insights and opportunities from an alternative mammal

The genome of a Gondwanan mammal

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