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A new reference genome assembly for the microcrustacean Daphnia pulex

Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman UGent, Xiaoqian Jiang, Matthew S Ackerman, Jacqueline Lopez, Brent Harker, R Taylor Raborn, W Kelley Thomas, et al. (2017) G3-GENES GENOMES GENETICS. 7(5). p.1405-1416
abstract
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 similar to 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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
genome annotation, effective population size, gene number, intron, mobile elements, TRANSPOSABLE ELEMENTS, LTR RETROTRANSPOSONS, EUKARYOTIC GENOMES, SEQUENCE DATA, EVOLUTION, POPULATIONS, ANNOTATION, RATES, ALIGNMENT, DATABASE
journal title
G3-GENES GENOMES GENETICS
G3-Genes Genomes Genet.
volume
7
issue
5
pages
1405 - 1416
Web of Science type
Article
Web of Science id
000400822200003
ISSN
2160-1836
DOI
10.1534/g3.116.038638
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8511350
handle
http://hdl.handle.net/1854/LU-8511350
date created
2017-02-27 07:53:22
date last changed
2018-03-05 11:41:32
@article{8511350,
  abstract     = {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 {\textrangle}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 {\textrangle}60\% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with similar to 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.},
  author       = {Ye, Zhiqiang and Xu, Sen and Spitze, Ken and Asselman, Jana and Jiang, Xiaoqian and Ackerman, Matthew S and Lopez, Jacqueline and Harker, Brent and Raborn, R Taylor and Thomas, W Kelley and Ramsdell, Jordan and Pfrender, Michael E and Lynch, Michael},
  issn         = {2160-1836},
  journal      = {G3-GENES GENOMES GENETICS},
  keyword      = {genome annotation,effective population size,gene number,intron,mobile elements,TRANSPOSABLE ELEMENTS,LTR RETROTRANSPOSONS,EUKARYOTIC GENOMES,SEQUENCE DATA,EVOLUTION,POPULATIONS,ANNOTATION,RATES,ALIGNMENT,DATABASE},
  language     = {eng},
  number       = {5},
  pages        = {1405--1416},
  title        = {A new reference genome assembly for the microcrustacean Daphnia pulex},
  url          = {http://dx.doi.org/10.1534/g3.116.038638},
  volume       = {7},
  year         = {2017},
}

Chicago
Ye, Zhiqiang, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S Ackerman, Jacqueline Lopez, et al. 2017. “A New Reference Genome Assembly for the Microcrustacean Daphnia Pulex.” G3-GENES GENOMES GENETICS 7 (5): 1405–1416.
APA
Ye, Zhiqiang, Xu, S., Spitze, K., Asselman, J., Jiang, X., Ackerman, M. S., Lopez, J., et al. (2017). A new reference genome assembly for the microcrustacean Daphnia pulex. G3-GENES GENOMES GENETICS, 7(5), 1405–1416.
Vancouver
1.
Ye Z, Xu S, Spitze K, Asselman J, Jiang X, Ackerman MS, et al. A new reference genome assembly for the microcrustacean Daphnia pulex. G3-GENES GENOMES GENETICS. 2017;7(5):1405–16.
MLA
Ye, Zhiqiang, Sen Xu, Ken Spitze, et al. “A New Reference Genome Assembly for the Microcrustacean Daphnia Pulex.” G3-GENES GENOMES GENETICS 7.5 (2017): 1405–1416. Print.