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Are we there yet? : reliably estimating the completeness of plant genome sequences

Elisabeth Veeckman UGent, Tom Ruttink and Klaas Vandepoele UGent (2016) PLANT CELL. 28(8). p.1759-1768
abstract
Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes. Most genome projects have a dual purpose: delivering a contiguous, complete genome assembly and creating a full catalog of correctly predicted genes. Frequently, the completeness of a species' gene catalog is measured using a set of marker genes that are expected to be present. This expectation can be defined along an evolutionary gradient, ranging from highly conserved genes to species-specific genes. Large-scale population resequencing studies have revealed that gene space is fairly variable even between closely related individuals, which limits the definition of the expected gene space, and, consequently, the accuracy of estimates used to assess genome and gene space completeness. We argue that, based on the desired applications of a genome sequencing project, different completeness scores for the genome assembly and/or gene space should be determined. Using examples from several dicot and monocot genomes, we outline some pitfalls and recommendations regarding methods to estimate completeness during different steps of genome assembly and annotation.
Please use this url to cite or link to this publication:
author
organization
year
type
misc (editorialMaterial)
publication status
published
subject
keyword
ARABIDOPSIS-THALIANA, DISPENSABLE GENOME, ANNOTATION, EVOLUTION, PROJECT, SIZE, TOOL
in
PLANT CELL
Plant Cell
volume
28
issue
8
pages
1759 - 1768
Web of Science type
Editorial Material
Web of Science id
000386169200003
JCR category
PLANT SCIENCES
JCR impact factor
8.688 (2016)
JCR rank
6/211 (2016)
JCR quartile
1 (2016)
ISSN
1040-4651
DOI
10.1105/tpc.16.00349
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
V
copyright statement
I have retained and own the full copyright for this publication
id
8510552
handle
http://hdl.handle.net/1854/LU-8510552
date created
2017-02-21 10:29:37
date last changed
2017-03-01 13:07:26
@misc{8510552,
  abstract     = {Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes. Most genome projects have a dual purpose: delivering a contiguous, complete genome assembly and creating a full catalog of correctly predicted genes. Frequently, the completeness of a species' gene catalog is measured using a set of marker genes that are expected to be present. This expectation can be defined along an evolutionary gradient, ranging from highly conserved genes to species-specific genes. Large-scale population resequencing studies have revealed that gene space is fairly variable even between closely related individuals, which limits the definition of the expected gene space, and, consequently, the accuracy of estimates used to assess genome and gene space completeness. We argue that, based on the desired applications of a genome sequencing project, different completeness scores for the genome assembly and/or gene space should be determined. Using examples from several dicot and monocot genomes, we outline some pitfalls and recommendations regarding methods to estimate completeness during different steps of genome assembly and annotation.},
  author       = {Veeckman, Elisabeth and Ruttink, Tom and Vandepoele, Klaas},
  issn         = {1040-4651},
  keyword      = {ARABIDOPSIS-THALIANA,DISPENSABLE GENOME,ANNOTATION,EVOLUTION,PROJECT,SIZE,TOOL},
  language     = {eng},
  number       = {8},
  pages        = {1759--1768},
  series       = {PLANT CELL},
  title        = {Are we there yet? : reliably estimating the completeness of plant genome sequences},
  url          = {http://dx.doi.org/10.1105/tpc.16.00349},
  volume       = {28},
  year         = {2016},
}

Chicago
Veeckman, Elisabeth, Tom Ruttink, and Klaas Vandepoele. 2016. “Are We There yet? : Reliably Estimating the Completeness of Plant Genome Sequences.” Plant Cell.
APA
Veeckman, Elisabeth, Ruttink, T., & Vandepoele, K. (2016). Are we there yet? : reliably estimating the completeness of plant genome sequences. PLANT CELL.
Vancouver
1.
Veeckman E, Ruttink T, Vandepoele K. Are we there yet? : reliably estimating the completeness of plant genome sequences. PLANT CELL. 2016. p. 1759–68.
MLA
Veeckman, Elisabeth, Tom Ruttink, and Klaas Vandepoele. “Are We There yet? : Reliably Estimating the Completeness of Plant Genome Sequences.” PLANT CELL 2016 : 1759–1768. Print.