Massive genomic variation and strong selection in Arabidopsis
thaliana lines from Sweden

J 2013

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

LONG, Quan, Fernando A. RABANAL, Dazhe MENG, Christian D. HUBER, Ashley FARLOW et. al.

Basic information

Original name

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Authors

LONG, Quan (40 Austria), Fernando A. RABANAL (40 Austria), Dazhe MENG (840 United States of America), Christian D. HUBER (40 Austria), Ashley FARLOW (40 Austria), Alexander PLATZER (40 Austria), Qingrun ZHANG (40 Austria), Bjarni J. VILHJÁLMSSON (840 United States of America), Arthur KORTE (40 Austria), Viktoria NIZHYNSKA (40 Austria), Viktor VORONIN (40 Austria), Pamela KORTE (40 Austria), Laura SEDMAN (40 Austria), Terezie MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution), Uemit SEREN (40 Austria), Ines HELLMANN (40 Austria) and Magnus NORDBORG (840 United States of America)

Edition

Nature Genetics, New York, Nature Publishing Group, 2013, 1061-4036

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 29.648

RIV identification code

RIV/00216224:14740/13:00066452

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/ng.2678

UT WoS

000322374900010

Keywords in English

RIBOSOMAL-RNA GENES; LINKAGE DISEQUILIBRIUM; WIDE ASSOCIATION; NATURAL VARIATION; DNA; POPULATIONS; SEQUENCE; POLYMORPHISM; METHYLATION; ACCESSIONS

Abstract

V originále

Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.

Links

GAP506/12/0668, research and development project

Name: Trendy v evoluci polyploidních komplexů: obdobné nebo odlišné příběhy u třech skupin z čeledi Brassicaceae?

Investor: Czech Science Foundation

GBP501/12/G090, research and development project

Name: Evoluce a funkce komplexních genomů rostlin

Citovat

LONG, Quan, Fernando A. RABANAL, Dazhe MENG, Christian D. HUBER, Ashley FARLOW, Alexander PLATZER, Qingrun ZHANG, Bjarni J. VILHJÁLMSSON, Arthur KORTE, Viktoria NIZHYNSKA, Viktor VORONIN, Pamela KORTE, Laura SEDMAN, Terezie MANDÁKOVÁ, Martin LYSÁK, Uemit SEREN, Ines HELLMANN and Magnus NORDBORG. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nature Genetics. New York: Nature Publishing Group, 2013, vol. 45, No 8, p. 884-"U218", 8 pp. ISSN 1061-4036. Available from: https://dx.doi.org/10.1038/ng.2678.

@article{1126885,
   author = {Long, Quan and Rabanal, Fernando A. and Meng, Dazhe and Huber, Christian D. and Farlow, Ashley and Platzer, Alexander and Zhang, Qingrun and Vilhjálmsson, Bjarni J. and Korte, Arthur and Nizhynska, Viktoria and Voronin, Viktor and Korte, Pamela and Sedman, Laura and Mandáková, Terezie and Lysák, Martin and Seren, Uemit and Hellmann, Ines and Nordborg, Magnus},
   article_location = {New York},
   article_number = {8},
   doi = {http://dx.doi.org/10.1038/ng.2678},
   keywords = {RIBOSOMAL-RNA GENES; LINKAGE DISEQUILIBRIUM; WIDE ASSOCIATION; NATURAL VARIATION; DNA; POPULATIONS; SEQUENCE; POLYMORPHISM; METHYLATION; ACCESSIONS},
   language = {eng},
   issn = {1061-4036},
   journal = {Nature Genetics},
   title = {Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden},
   url = {http://www.nature.com/ng/journal/v45/n8/full/ng.2678.html},
   volume = {45},
   year = {2013}
}

TY  - JOUR
ID  - 1126885
AU  - Long, Quan - Rabanal, Fernando A. - Meng, Dazhe - Huber, Christian D. - Farlow, Ashley - Platzer, Alexander - Zhang, Qingrun - Vilhjálmsson, Bjarni J. - Korte, Arthur - Nizhynska, Viktoria - Voronin, Viktor - Korte, Pamela - Sedman, Laura - Mandáková, Terezie - Lysák, Martin - Seren, Uemit - Hellmann, Ines - Nordborg, Magnus
PY  - 2013
TI  - Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
JF  - Nature Genetics
VL  - 45
IS  - 8
SP  - 884-"U218"
EP  - 884-"U218"
PB  - Nature Publishing Group
SN  - 10614036
KW  - RIBOSOMAL-RNA GENES
KW  - LINKAGE DISEQUILIBRIUM
KW  - WIDE ASSOCIATION
KW  - NATURAL VARIATION
KW  - DNA
KW  - POPULATIONS
KW  - SEQUENCE
KW  - POLYMORPHISM
KW  - METHYLATION
KW  - ACCESSIONS
UR  - http://www.nature.com/ng/journal/v45/n8/full/ng.2678.html
L2  - http://www.nature.com/ng/journal/v45/n8/full/ng.2678.html
N2  - Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.
ER  -

LONG, Quan, Fernando A. RABANAL, Dazhe MENG, Christian D. HUBER, Ashley FARLOW, Alexander PLATZER, Qingrun ZHANG, Bjarni J. VILHJÁLMSSON, Arthur KORTE, Viktoria NIZHYNSKA, Viktor VORONIN, Pamela KORTE, Laura SEDMAN, Terezie MANDÁKOVÁ, Martin LYSÁK, Uemit SEREN, Ines HELLMANN and Magnus NORDBORG. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. \textit{Nature Genetics}. New York: Nature Publishing Group, 2013, vol.~45, No~8, p.~884-''U218'', 8 pp. ISSN~1061-4036. Available from: https://dx.doi.org/10.1038/ng.2678.

Detailed Information on Publication Record