TY - JOUR
T1 - A new reference genome assembly for the microcrustacean Daphnia pulex
AU - Ye, Zhiqiang
AU - Xu, Sen
AU - Spitze, Ken
AU - Asselman, Jana
AU - Jiang, Xiaoqian
AU - Ackerman, Matthew S.
AU - Lopez, Jacqueline
AU - Harker, Brent
AU - Raborn, R. Taylor
AU - Thomas, W. Kelley
AU - Ramsdell, Jordan
AU - Pfrender, Michael E.
AU - Lynch, Michael
N1 - Funding Information:
We thank Kim Young for maintaining Daphnia cultures and Illumina, Inc. for assistance with the Long Synthetic Read methodology. This work is supported by National Institutes of Health grant R01GM101672 to M.L. J.A. was the recipient of a Belgian American Education Foundation fellowship for research. The authors confirm that there are no known conflicts of interest associated with this publication.
Publisher Copyright:
© 2017 Ye et al.
PY - 2017/5/1
Y1 - 2017/5/1
N2 - Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
AB - Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
KW - Effective population size
KW - Gene number intron
KW - Genome annotation
KW - Mobile elements
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U2 - 10.1534/g3.116.038638
DO - 10.1534/g3.116.038638
M3 - Article
C2 - 28235826
AN - SCOPUS:85019175682
SN - 2160-1836
VL - 7
SP - 1405
EP - 1416
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 5
ER -