An analysis of the gene complement of a marsupial,<i>Monodelphis domestica</i>: Evolution of lineage-specific genes and giant chromosomes

Goodstadt, Leo; Heger, Andreas; Webber, Caleb; Ponting, Chris P.

doi:10.1101/gr.6093907

Cited by 67 publications

(39 citation statements)

References 70 publications

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“…Overall this resulted in 18,527 protein-coding genes being predicted from the current platypus assembly. The number of platypus protein-coding genes thus is similar to estimates (18,600-20,800) for human and opossum 28,29 .…”

Section: Gene Evolutionsupporting

confidence: 64%

Genome analysis of the platypus reveals unique signatures of evolution

Warren¹,

Hillier²,

Graves³

et al. 2008

Nature

614

327

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A list of authors and their affiliations appears at the end of the paperWe present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

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Section: Gene Evolutionsupporting

confidence: 64%

Genome analysis of the platypus reveals unique signatures of evolution

Warren¹,

Hillier²,

Graves³

et al. 2008

Nature

614

327

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“…This is the opposite to what is observed within Eutheria 10 , but is consistent with the expectation that the higher G1C-content and recombination rate on the opossum X chromosome relative to its autosomes implies a higher rate of mutation 47 . A similar elevation can also be detected in subtelomeric regions 34 . Innovation and turnover in gene families.…”

Section: Genessupporting

confidence: 51%

“…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).…”

Section: Genesmentioning

confidence: 99%

“…Gene catalogue. 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). Regularly updated annotations can be obtained from public databases (http://www.ensembl.org and http://genome.ucsc.edu).…”

Section: Genesmentioning

confidence: 99%

“…Extensions to these findings, as well as additional topics, are reported in a series of companion papers [31][32][33][34][35][36][37][38][39][40][41] .…”

mentioning

confidence: 99%

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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

Self Cite

664

592

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We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

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Evolution and Characteristics of the Opossum Genome

Samollow

2009

Encyclopedia of Life Sciences

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The opossum genome sequence furnishes a critical comparator for examining the evolutionary histories of vertebrate genomes in general, and provides the most appropriate outgroup sequence for establishing the relative antiquity or novelty of genetic features among the major lineages of eutherian (‘placental’) mammals. Comparative analyses using the opossum genome have already provided a wealth of 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. This article summarizes key features of the opossum genome and discusses their implications for better understanding the varied processes that contribute to genome evolution and how changes in structural organization, complexity, and molecular functions of mammalian (and other) genomes can lead to differences in gene regulation, expression, and action among and within species. Key concepts: Because the pace of evolutionary change varies for different classes of genomic elements, the power of comparative genomic analysis is dependent on the availability of genomic data from organisms occupying key phylogenetic positions that enable comparisons of both slow and fast evolving genomic features. Metatherian (marsupial) and eutherian (placental) mammals are each other's closest relatives. During divergence from their common ancestor they evolved distinctive morphologic, physiologic, and genetic variations on the elemental mammalian patterns. These distinctions hold great potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Representing the Metatheria, the opossum genome furnishes a crucial reference for examining the evolutionary histories of vertebrate genomes in general, and provides the most appropriate outgroup sequence for establishing ancestral versus derived polarity for genomic and genetic features among the major lineages of eutherian mammals. The opossum genome sequence has provided 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 opossum genome is comprised of eight very large autosomes and a sex chromosome (X or Y), and exhibits extremely low levels of meiotic recombination relative to other mammalian genomes examined. The opossum genome exhibits the lowest levels of G and C nucleotides known among sequenced amniotes. At least 52% of the opossum genome is composed of interspersed repeat family elements—the highest level known from sequenced amniotes. Low recombination rate may contribute to the unusual nucleotide composition and the high levels of interspersed repeat elements in the opossum genome. The protein‐coding gene complement of the opossum genome is very similar to that of eutherian mammals and other vertebrates. Conserved noncoding genomic elements (CNEs) show high levels of novelty between opossum and eutherian genomes and strong lineage specificity among eutherian clades. This finding strengthens the idea that in mammalian evolution alterations in the repertoires of noncoding elements that regulate protein‐coding gene function may be more important than changes in the structures or numbers of protein‐coding genes. The opossum genome has provided new evidence regarding the structure of the ancestral eutherian karyotype and the evolution of genomic imprinting. It also furnishes new tools to study the evolution and function of the mammalian immune system and the phenomenon of X‐chromosome inactivation.

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An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Cited by 67 publications

References 70 publications

Genome analysis of the platypus reveals unique signatures of evolution

Genome analysis of the platypus reveals unique signatures of evolution

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Evolution and Characteristics of the Opossum Genome

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