Global Brassicaceae phylogeny based on filtering of 1,000-gene
dataset

J 2023

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

HENDRIKS, Kasper P, Christiane KIEFER, Ihsan A AL-SHEHBAZ, C Donovan BAILEY, van Huysduynen Alex HOOFT et. al.

Základní údaje

Originální název

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Autoři

HENDRIKS, Kasper P, Christiane KIEFER, Ihsan A AL-SHEHBAZ, C Donovan BAILEY, van Huysduynen Alex HOOFT, Lachezar A NIKOLOV, Lars NAUHEIMER, Alexandre R ZUNTINI, Dmitry A GERMAN, Andreas FRANZKE, Marcus A KOCH, Martin LYSÁK (203 Česká republika, domácí), Oscar TORO-NUNEZ, Baris OZUDOGRU, Vanessa R INVERNON, Nora WALDEN, Olivier MAURIN, Nikolai M HAY, Philip SHUSHKOV, Terezie MALÍK MANDÁKOVÁ (203 Česká republika, domácí), M Eric SCHRANZ, Mats THULIN, Michael D WINDHAM, Ivana RESETNIK, Stanislav SPANIEL, Elfy LY, J Chris PIRES, Alex HARKESS, Barbara NEUFFER, Robert VOGT, Christian BRAUCHLER, Heimo RAINER, Steven B JANSSENS, Michaela SCHMULL, Alan FORREST, Alessia GUGGISBERG, Sue ZMARZTY, Brendan J LEPSCHI, Neville SCARLETT, Fred W STAUFFER, Ines SCHONBERGER, Peter HEENAN, William J BAKER, Felix FOREST, Klaus MUMMENHOFF (garant) a Frederic LENS

Vydání

Current Biology, CAMBRIDGE, CELL PRESS, 2023, 0960-9822

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.200 v roce 2022

Kód RIV

RIV/00216224:14740/23:00134399

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1016/j.cub.2023.08.026

UT WoS

001098689800001

Klíčová slova anglicky

MULTIPLE SEQUENCE ALIGNMENT; MOLECULAR SYSTEMATICS; PENALIZED LIKELIHOOD; EVOLUTION; DIVERSIFICATION; BIOGEOGRAPHY; ARABIDOPSIS; PLANT DIPLOIDIZATION; TRANSITION

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 2. 2024 14:28, Mgr. Eva Dubská

Anotace

V originále

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.

Návaznosti

GA21-03909S, projekt VaV

Název: Odhalení evolučních tajů lničky seté a příbuzných druhů

Investor: Grantová agentura ČR, Odhalení evolučních tajů lničky seté a příbuzných druhů

GA21-06839S, projekt VaV

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

Investor: Grantová agentura ČR, The origin and evolution of apomixis-related chromosomes in Boechera (Brassicaceae)

Citovat

HENDRIKS, Kasper P, Christiane KIEFER, Ihsan A AL-SHEHBAZ, C Donovan BAILEY, van Huysduynen Alex HOOFT, Lachezar A NIKOLOV, Lars NAUHEIMER, Alexandre R ZUNTINI, Dmitry A GERMAN, Andreas FRANZKE, Marcus A KOCH, Martin LYSÁK, Oscar TORO-NUNEZ, Baris OZUDOGRU, Vanessa R INVERNON, Nora WALDEN, Olivier MAURIN, Nikolai M HAY, Philip SHUSHKOV, Terezie MALÍK MANDÁKOVÁ, M Eric SCHRANZ, Mats THULIN, Michael D WINDHAM, Ivana RESETNIK, Stanislav SPANIEL, Elfy LY, J Chris PIRES, Alex HARKESS, Barbara NEUFFER, Robert VOGT, Christian BRAUCHLER, Heimo RAINER, Steven B JANSSENS, Michaela SCHMULL, Alan FORREST, Alessia GUGGISBERG, Sue ZMARZTY, Brendan J LEPSCHI, Neville SCARLETT, Fred W STAUFFER, Ines SCHONBERGER, Peter HEENAN, William J BAKER, Felix FOREST, Klaus MUMMENHOFF a Frederic LENS. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Current Biology. CAMBRIDGE: CELL PRESS, 2023, roč. 33, č. 19, s. 4052-4075. ISSN 0960-9822. Dostupné z: https://dx.doi.org/10.1016/j.cub.2023.08.026.

@article{2369679,
   author = {Hendriks, Kasper P and Kiefer, Christiane and AlandShehbaz, Ihsan A and Bailey, C Donovan and Hooft, van Huysduynen Alex and Nikolov, Lachezar A and Nauheimer, Lars and Zuntini, Alexandre R and German, Dmitry A and Franzke, Andreas and Koch, Marcus A and Lysák, Martin and ToroandNunez, Oscar and Ozudogru, Baris and Invernon, Vanessa R and Walden, Nora and Maurin, Olivier and Hay, Nikolai M and Shushkov, Philip and Malík Mandáková, Terezie and Schranz, M Eric and Thulin, Mats and Windham, Michael D and Resetnik, Ivana and Spaniel, Stanislav and Ly, Elfy and Pires, J Chris and Harkess, Alex and Neuffer, Barbara and Vogt, Robert and Brauchler, Christian and Rainer, Heimo and Janssens, Steven B and Schmull, Michaela and Forrest, Alan and Guggisberg, Alessia and Zmarzty, Sue and Lepschi, Brendan J and Scarlett, Neville and Stauffer, Fred W and Schonberger, Ines and Heenan, Peter and Baker, William J and Forest, Felix and Mummenhoff, Klaus and Lens, Frederic},
   article_location = {CAMBRIDGE},
   article_number = {19},
   doi = {http://dx.doi.org/10.1016/j.cub.2023.08.026},
   keywords = {MULTIPLE SEQUENCE ALIGNMENT; MOLECULAR SYSTEMATICS; PENALIZED LIKELIHOOD; EVOLUTION; DIVERSIFICATION; BIOGEOGRAPHY; ARABIDOPSIS; PLANT DIPLOIDIZATION; TRANSITION},
   language = {eng},
   issn = {0960-9822},
   journal = {Current Biology},
   title = {Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset},
   url = {https://www.sciencedirect.com/science/article/pii/S0960982223010692?via%3Dihub},
   volume = {33},
   year = {2023}
}

TY  - JOUR
ID  - 2369679
AU  - Hendriks, Kasper P - Kiefer, Christiane - Al-Shehbaz, Ihsan A - Bailey, C Donovan - Hooft, van Huysduynen Alex - Nikolov, Lachezar A - Nauheimer, Lars - Zuntini, Alexandre R - German, Dmitry A - Franzke, Andreas - Koch, Marcus A - Lysák, Martin - Toro-Nunez, Oscar - Ozudogru, Baris - Invernon, Vanessa R - Walden, Nora - Maurin, Olivier - Hay, Nikolai M - Shushkov, Philip - Malík Mandáková, Terezie - Schranz, M Eric - Thulin, Mats - Windham, Michael D - Resetnik, Ivana - Spaniel, Stanislav - Ly, Elfy - Pires, J Chris - Harkess, Alex - Neuffer, Barbara - Vogt, Robert - Brauchler, Christian - Rainer, Heimo - Janssens, Steven B - Schmull, Michaela - Forrest, Alan - Guggisberg, Alessia - Zmarzty, Sue - Lepschi, Brendan J - Scarlett, Neville - Stauffer, Fred W - Schonberger, Ines - Heenan, Peter - Baker, William J - Forest, Felix - Mummenhoff, Klaus - Lens, Frederic
PY  - 2023
TI  - Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
JF  - Current Biology
VL  - 33
IS  - 19
SP  - 4052-4075
EP  - 4052-4075
PB  - CELL PRESS
SN  - 09609822
KW  - MULTIPLE SEQUENCE ALIGNMENT
KW  - MOLECULAR SYSTEMATICS
KW  - PENALIZED LIKELIHOOD
KW  - EVOLUTION
KW  - DIVERSIFICATION
KW  - BIOGEOGRAPHY
KW  - ARABIDOPSIS
KW  - PLANT DIPLOIDIZATION
KW  - TRANSITION
UR  - https://www.sciencedirect.com/science/article/pii/S0960982223010692?via%3Dihub
N2  - The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
ER  -

HENDRIKS, Kasper P, Christiane KIEFER, Ihsan A AL-SHEHBAZ, C Donovan BAILEY, van Huysduynen Alex HOOFT, Lachezar A NIKOLOV, Lars NAUHEIMER, Alexandre R ZUNTINI, Dmitry A GERMAN, Andreas FRANZKE, Marcus A KOCH, Martin LYSÁK, Oscar TORO-NUNEZ, Baris OZUDOGRU, Vanessa R INVERNON, Nora WALDEN, Olivier MAURIN, Nikolai M HAY, Philip SHUSHKOV, Terezie MALÍK MANDÁKOVÁ, M Eric SCHRANZ, Mats THULIN, Michael D WINDHAM, Ivana RESETNIK, Stanislav SPANIEL, Elfy LY, J Chris PIRES, Alex HARKESS, Barbara NEUFFER, Robert VOGT, Christian BRAUCHLER, Heimo RAINER, Steven B JANSSENS, Michaela SCHMULL, Alan FORREST, Alessia GUGGISBERG, Sue ZMARZTY, Brendan J LEPSCHI, Neville SCARLETT, Fred W STAUFFER, Ines SCHONBERGER, Peter HEENAN, William J BAKER, Felix FOREST, Klaus MUMMENHOFF a Frederic LENS. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. \textit{Current Biology}. CAMBRIDGE: CELL PRESS, 2023, roč.~33, č.~19, s.~4052-4075. ISSN~0960-9822. Dostupné z: https://dx.doi.org/10.1016/j.cub.2023.08.026.

Podrobný výpis o publikaci