Genomic Blocks in Aethionema arabicum Support Arabideae as Next
Diverging Clade in Brassicaceae

J 2020

Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

WALDEN, N., T.P. NGUYEN, Terezie MANDÁKOVÁ, Martin LYSÁK, M.E. SCHRANZ et. al.

Basic information

Original name

Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

Authors

WALDEN, N., T.P. NGUYEN, Terezie MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution) and M.E. SCHRANZ

Edition

Frontiers in Plant Science, 2020, 1664-462X

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.753

RIV identification code

RIV/00216224:14740/20:00113906

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.3389/fpls.2020.00719

UT WoS

000542984700001

Keywords in English

Aethionema; Brassicaceae; comparative genomics; genomic blocks; synteny; Arabideae

Abstract

V originále

The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.

Links

GA15-18545S, research and development project

Name: Evoluce genomu a časoprostorová diversita v tribu Arabideae

Investor: Czech Science Foundation

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

WALDEN, N., T.P. NGUYEN, Terezie MANDÁKOVÁ, Martin LYSÁK and M.E. SCHRANZ. Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae. Frontiers in Plant Science. 2020, vol. 11, JUN, p. 719-727. ISSN 1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2020.00719.

@article{1660018,
   author = {Walden, N. and Nguyen, T.P. and Mandáková, Terezie and Lysák, Martin and Schranz, M.E.},
   article_number = {JUN},
   doi = {http://dx.doi.org/10.3389/fpls.2020.00719},
   keywords = {Aethionema; Brassicaceae; comparative genomics; genomic blocks; synteny; Arabideae},
   language = {eng},
   issn = {1664-462X},
   journal = {Frontiers in Plant Science},
   title = {Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae},
   url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.00719/full},
   volume = {11},
   year = {2020}
}

TY  - JOUR
ID  - 1660018
AU  - Walden, N. - Nguyen, T.P. - Mandáková, Terezie - Lysák, Martin - Schranz, M.E.
PY  - 2020
TI  - Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae
JF  - Frontiers in Plant Science
VL  - 11
IS  - JUN
SP  - 719
EP  - 719
SN  - 1664462X
KW  - Aethionema
KW  - Brassicaceae
KW  - comparative genomics
KW  - genomic blocks
KW  - synteny
KW  - Arabideae
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2020.00719/full
L2  - https://www.frontiersin.org/articles/10.3389/fpls.2020.00719/full
N2  - The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.
ER  -

WALDEN, N., T.P. NGUYEN, Terezie MANDÁKOVÁ, Martin LYSÁK and M.E. SCHRANZ. Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae. \textit{Frontiers in Plant Science}. 2020, vol.~11, JUN, p.~719-727. ISSN~1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2020.00719.

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