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Accepted (AM)Open Access (License Unspecified), Open
Journal article
Transcriptome resources for the white‐footed mouse ( Peromyscus leucopus ): new genomic tools for investigating ecologically divergent urban and rural populations
Molecular ecology resources, v 15(2), pp 382-394
Mar 2015
PMID: 24980186
Abstract
Abstract
Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of nonmodel species. We utilized two next‐generation sequencing (
NGS
) platforms, 454 and
SOL
i
D
5500
XL
, to assemble low‐coverage transcriptomes of the white‐footed mouse (
P
eromyscus leucopus
), a widespread and abundant native rodent in eastern
N
orth
A
merica. We sequenced liver m
RNA
transcripts from multiple individuals collected from urban populations in
N
ew
Y
ork
C
ity and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1 080 065 954
SOL
i
D
5500
XL
(75 bp) reads and 3 052 640 454
GS FLX
+ reads. The reference contained 40 908 contigs with a
N
50 = 1044 bp and a total content of 30.06
M
egabases (
M
b). Contigs were annotated from
M
us musculus
(39.96% annotated)
U
niprot databases. We identified 104 655 high‐quality single nucleotide polymorphisms (
SNP
s) and 65 single sequence repeats (
SSR
s) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using
N
orth
A
merican
P
eromyscus
species as emerging model systems for ecological genetics and adaptation.
Metrics
Details
- Title
- Transcriptome resources for the white‐footed mouse ( Peromyscus leucopus ): new genomic tools for investigating ecologically divergent urban and rural populations
- Creators
- Stephen E. Harris - The Graduate Center, CUNYRachel J. O'Neill - Molecular & Cell Biology University of Connecticut Storrs CT 06269 USAJason Munshi-South - Fordham University
- Publication Details
- Molecular ecology resources, v 15(2), pp 382-394
- Publisher
- Wiley
- Number of pages
- 13
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES)
- Web of Science ID
- WOS:000349819000016
- Scopus ID
- 2-s2.0-84922529616
- Other Identifier
- 991021903954404721
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Ecology
- Evolutionary Biology