A Hyb-Seq phylogeny of Boechera and related genera using a
combination of Angiosperms353 and Brassicaceae-specific bait
sets

J 2023

A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets

HAY, Nikolai M, Michael D WINDHAM, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Kasper P. HENDRIKS et. al.

Basic information

Original name

A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets

Authors

HAY, Nikolai M (guarantor), Michael D WINDHAM, Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Martin LYSÁK (203 Czech Republic, belonging to the institution), Kasper P. HENDRIKS, Klaus MUMMENHOFF, Frederic LENS, Kathleen M. PRYER and C. Donovan BAILEY

Edition

American Journal of Botany, 1537-2197, Wiley, 2023, 0002-9122

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.000 in 2022

RIV identification code

RIV/00216224:14740/23:00133319

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/ajb2.16226

UT WoS

001081536700001

Keywords in English

angiosperms; Boechera; Boechereae; Brassicaceae; Hyb-Seq; phylogenomics; supermatrix

Abstract

V originále

Premise: Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. Methods: To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. ResultsOur analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. Conclusions: This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.

Links

GA21-06839S, research and development project

Name: Vznik a evoluce chromozomů spojených s apomixií v rodu Boechera (Brassicaceae)

Investor: Czech Science Foundation

Citovat

HAY, Nikolai M, Michael D WINDHAM, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Kasper P. HENDRIKS, Klaus MUMMENHOFF, Frederic LENS, Kathleen M. PRYER and C. Donovan BAILEY. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. American Journal of Botany. 1537-2197: Wiley, 2023, vol. 110, No 10, p. 1-20. ISSN 0002-9122. Available from: https://dx.doi.org/10.1002/ajb2.16226.

@article{2367599,
   author = {Hay, Nikolai M and Windham, Michael D and Malík Mandáková, Terezie and Lysák, Martin and Hendriks, Kasper P. and Mummenhoff, Klaus and Lens, Frederic and Pryer, Kathleen M. and Bailey, C. Donovan},
   article_location = {1537-2197},
   article_number = {10},
   doi = {http://dx.doi.org/10.1002/ajb2.16226},
   keywords = {angiosperms; Boechera; Boechereae; Brassicaceae; Hyb-Seq; phylogenomics; supermatrix},
   language = {eng},
   issn = {0002-9122},
   journal = {American Journal of Botany},
   title = {A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets},
   url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.16226},
   volume = {110},
   year = {2023}
}

TY  - JOUR
ID  - 2367599
AU  - Hay, Nikolai M - Windham, Michael D - Malík Mandáková, Terezie - Lysák, Martin - Hendriks, Kasper P. - Mummenhoff, Klaus - Lens, Frederic - Pryer, Kathleen M. - Bailey, C. Donovan
PY  - 2023
TI  - A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets
JF  - American Journal of Botany
VL  - 110
IS  - 10
SP  - 1-20
EP  - 1-20
PB  - Wiley
SN  - 00029122
KW  - angiosperms
KW  - Boechera
KW  - Boechereae
KW  - Brassicaceae
KW  - Hyb-Seq
KW  - phylogenomics
KW  - supermatrix
UR  - https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.16226
N2  - Premise: Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. Methods: To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. ResultsOur analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. Conclusions: This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
ER  -

HAY, Nikolai M, Michael D WINDHAM, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Kasper P. HENDRIKS, Klaus MUMMENHOFF, Frederic LENS, Kathleen M. PRYER and C. Donovan BAILEY. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. \textit{American Journal of Botany}. 1537-2197: Wiley, 2023, vol.~110, No~10, p.~1-20. ISSN~0002-9122. Available from: https://dx.doi.org/10.1002/ajb2.16226.

Detailed Information on Publication Record