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

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Nature (Impact Factor: 41.46). 06/2007; 447(7141):167-77.
Source: PubMed


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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    • "e relatively low ( 0 . 27 subs / site ) only because half of the genomic positions assigned to this repeat family were evolutionarily constrained . Overall , the pattern of TE enrichment within ACs is consistent with a model in which all TE families possess approximately the same functional potential . As previously suggested ( Lowe at al . 2007 ; Mikkelsen et al . 2007 ) , the ancient repeat families that do show functional enrichment most likely do so because their non - constrained instances have decayed so much that they are no longer recognizable as TEs by RepeatMasker ."
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    ABSTRACT: Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions, and confirmed their robust functional signatures. 99.7% of ASC basepairs were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of non-repetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the 'gene-battery' model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes, and supports an elegantly simple new null model of TE exaptation.
    Genome Research 07/2014; Genome Res. 2014 Jul 20. pii: gr.168963.113.(pii: gr.168963.113.[Epub ahead of print]). DOI:10.1101/gr.168963.113 · 14.63 Impact Factor
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    • "In the laboratory, these animals have proven to be useful for a wide range of research questions, particularly studies of development, due in no small part to the early stage at which their offspring are born and the lack of a pouch, which makes offspring accessible (Saunders et al., 1989; Karlen et al., 2006; Karlen and Krubitzer, 2009). Furthermore, the short-tailed opossum was the first marsupial to have its genome sequenced, opening the door to many evolutionary and genetic studies (Mikkelsen et al., 2007). We recently assessed the visual acuity of opossums using the optokinetic test, which relies on the reflexive head movements that follow a moving stimulus (Dooley et al., 2012). "
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    ABSTRACT: The gray short-tailed opossum (Monodelphis domestica) is a nocturnal South American marsupial that has been gaining popularity as a laboratory animal. However, compared to traditional laboratory animals like rats, very little is known about its behavior, either in the wild or in a laboratory setting. Here we investigated the photic preference of the short-tailed opossum. Opossums were placed in a circular testing arena and allowed to move freely between dark (0 lux) and light (∼1.4, 40, or 400 lux) sides of the arena. In each of these conditions opossums spent significantly more time in the dark than in the illuminated side and a greater proportion of time in the dark than would be expected by chance. In the high-contrast (∼400 lux) illumination condition, the mean bout length (i.e., duration of one trip on the light or dark side) was significantly longer on the dark side than on the light side. When we examined the number of bouts greater than 30 and 60 s in duration, we found a significant difference between the light and dark sides in all light contrast conditions. These data indicate that the short-tailed opossum prefers the dark to the light, and can also detect very slight differences in light intensity. We conclude that although rats and opossums share many similar characteristics, including ecological niche, their divergent evolutionary heritage results in vastly different behavioral capabilities. Only by observing the behavioral capabilities and preferences of opossums will we be able to manipulate the experimental environment to best elicit and elucidate their behavior and alterations in behavior that can arise from experimental manipulations.
    Neuroscience 06/2014; 269:273–280. DOI:10.1016/j.neuroscience.2014.03.057 · 3.36 Impact Factor
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    • "We found some types of repetitive sequences were significantly increased in the rearrangement regions (Fig. 4b, Supplementary Table S12). This result is consistent with previous findings3132. Interestingly, the proportions of LINE_L1 and LTR_ERV1 increased, but the proportions of LINE_L2 and several other repetitive sequences decreased (Fig. 4c, Supplementary Table S13 to S16). "
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    ABSTRACT: Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.
    Scientific Reports 05/2014; 4:4958. DOI:10.1038/srep04958 · 5.58 Impact Factor
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