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Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area.

Harris SE, Munshi-South J, Obergfell C, O'Neill R - PLoS ONE (2013)

Bottom Line: From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus.These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments.This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Program in Ecology, Evolutionary Biology, & Behavior, The Graduate Center, City University of New York (CUNY), New York, New York, United States of America.

ABSTRACT
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar "urban adapter." We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

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Transcriptome alignment to reference rodent genomes.Number and distribution of contigs from P. leucopus transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) Rattus norvegicus. Blue = total number of genes per chromosome for Rattus. Red = number of aligned Peromyscus isotigs per Rattus chromosome. (b) Mus musculus. Blue = total number of genes per chromosome for Mus. Red = number of aligned Peromyscus isotigs per Mus chromosome.
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pone-0074938-g002: Transcriptome alignment to reference rodent genomes.Number and distribution of contigs from P. leucopus transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) Rattus norvegicus. Blue = total number of genes per chromosome for Rattus. Red = number of aligned Peromyscus isotigs per Rattus chromosome. (b) Mus musculus. Blue = total number of genes per chromosome for Mus. Red = number of aligned Peromyscus isotigs per Mus chromosome.

Mentions: Assembled mRNA transcripts from P. leucopus successfully mapped to both Mus and Rattus reference genomes and were distributed across all chromosomes for both references (Figure 2). There were 9,418 best BLAT hits between P. leucopus contigs and known Mus genes and 8,786 best hits with Rattus genes. The latest cDNA references include 35,900 genes for Mus (mm10) and 29,261 genes for Rattus (rn5), suggesting that full or partial coding sequence from approximately one-third to one-fourth of the P. leucopus transcriptome was sequenced. Given that many of the 15,000 contigs we assembled from our raw sequencing data may represent Peromyscus-specific genes not found in model rodent databases, the real proportion of the sequenced transcriptome may be much higher.


Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area.

Harris SE, Munshi-South J, Obergfell C, O'Neill R - PLoS ONE (2013)

Transcriptome alignment to reference rodent genomes.Number and distribution of contigs from P. leucopus transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) Rattus norvegicus. Blue = total number of genes per chromosome for Rattus. Red = number of aligned Peromyscus isotigs per Rattus chromosome. (b) Mus musculus. Blue = total number of genes per chromosome for Mus. Red = number of aligned Peromyscus isotigs per Mus chromosome.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756007&req=5

pone-0074938-g002: Transcriptome alignment to reference rodent genomes.Number and distribution of contigs from P. leucopus transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) Rattus norvegicus. Blue = total number of genes per chromosome for Rattus. Red = number of aligned Peromyscus isotigs per Rattus chromosome. (b) Mus musculus. Blue = total number of genes per chromosome for Mus. Red = number of aligned Peromyscus isotigs per Mus chromosome.
Mentions: Assembled mRNA transcripts from P. leucopus successfully mapped to both Mus and Rattus reference genomes and were distributed across all chromosomes for both references (Figure 2). There were 9,418 best BLAT hits between P. leucopus contigs and known Mus genes and 8,786 best hits with Rattus genes. The latest cDNA references include 35,900 genes for Mus (mm10) and 29,261 genes for Rattus (rn5), suggesting that full or partial coding sequence from approximately one-third to one-fourth of the P. leucopus transcriptome was sequenced. Given that many of the 15,000 contigs we assembled from our raw sequencing data may represent Peromyscus-specific genes not found in model rodent databases, the real proportion of the sequenced transcriptome may be much higher.

Bottom Line: From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus.These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments.This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Program in Ecology, Evolutionary Biology, & Behavior, The Graduate Center, City University of New York (CUNY), New York, New York, United States of America.

ABSTRACT
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar "urban adapter." We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

Show MeSH
Related in: MedlinePlus