An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
Open accessAbstract
The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chromosomes. Using PhyOP, we have established orthologs in Homo for 82% (15,250) of Monodelphis gene predictions. Those with single orthologs in each species exhibited a high median synonymous substitution rate (d S= 1.02), thereby explaining the relative paucity of aligned regions outside of coding sequences. Orthology assignments were used to construct a synteny map that illustrates the considerable fragmentation of Monodelphis and Homo karyotypes since their therian last common ancestor. Fifteen percent of Monodelphis genes are predicted, from their low divergence at synonymous sites, to have been duplicated in the metatherian lineage. The majority of Monodelphis-specific genes possess predicted roles in chemosensation, reproduction, adaptation to specific diets, and immunity. Using alignments of Monodelphis genes to sequences from either Homo or Trichosurus vulpecula(an Australian marsupial), we show that metatherian X chromosomes have elevated silent substitution rates and high G+C contents in comparison with both metatherian autosomes and eutherian chromosomes. Each of these elevations is also a feature of subtelomeric chromosomal regions. We attribute these observations to high rates of female-specific recombination near the chromosomal ends and within the X chromosome, which act to sustain or increase G+C levels by biased gene conversion. In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes.
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The number of platypus protein-coding genes is similar to estimates (18,600-20,800) for human and opossum.
“The number of platypus protein-coding genes thus is similar to estimates (18,600-20,800) for human and opossum 28,29 .”
From Genome analysis of the platypus reveals unique signatures of evolution (2008) · cites this paper as [29]
The opossum genome fits the predictions of the biased gene conversion model well.
“The opossum genome fits the predictions of this model well (see also refs 34, 35).”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [34]
An initial catalogue of 18,648 predicted protein-coding genes and 946 non-coding genes was generated for opossum.
“We generated an initial catalogue of 18,648 predicted protein-coding genes and 946 non-coding genes (primarily small nuclear RNA, small nucleolar RNA, microRNA and ribosomal RNA) in opossum 34 (Supplementary Note 9 and Supplementary Data).”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [34]
Patterns of evolution among duplicated genes in opossum largely mirror those observed in eutherians.
“The patterns of evolution among duplicated genes largely mirror those observed in eutherians 34,70 .”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [34]
The median Ks for orthologues located on the XCR is significantly elevated relative to orthologues located on autosomes in both species (1.2 versus 1.0; P < 10^-3).
“Notably, the median K S for orthologues located on the XCR is significantly elevated relative to orthologues located on autosomes in both species (1.2 versus 1.0; P , 10 23 ; see also refs 34, 35).”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [34]
Other major lineage-specific duplications in opossum involve the KRAB zinc-finger family and genes related to toxin degradation and dietary adaptations, including cytochrome P450 and various gastric enzymes.
“Other major lineage-specific duplications were found in the rapidly evolving KRAB zinc-finger family, and in genes related to toxin degradation and dietary adaptations, including cytochrome P450 and various gastric enzymes (see also ref. 34).”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [34]
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Genome analysis of the platypus reveals unique signatures of evolution
paper, A. L. O. A. A. T. A. A. A. T. E. O. T. (2008) · Nature · doi:10.1038/nature06936 · Cited by 719 · see citing works
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
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- Authors
- Goodstadt, L., Heger, A., Webber, C., & Ponting, C. P.
- Affiliations
- University of Oxford (GB)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-05-10
- Volume
- 17
- Issue
- 7
- Pages
- 969-981
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC1899124
- OpenAlex
- W2035178674
- Cited by
- 67
- References
- 71
- Citations by year
- 2024: 2 · 2023: 4 · 2022: 1 · 2021: 2 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 3 · 2014: 5 · 2013: 1 · 2012: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- Funders
- Medical Research Council
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Keywords
- Monodelphis domestica, marsupial genome, orthology, synteny, gene duplication, lineage-specific genes, X chromosome, GC content, biased gene conversion, subtelomeric regions, giant chromosomes, metatherians, immunity genes, Trichosurus vulpecula
- MeSH terms
- Animals, Chromosome Mapping, Humans, Pseudogenes, Sequence Homology, Nucleic Acid, Protein Engineering, Evolution, Molecular, Monodelphis
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