Mitoplastomic discordance in Brassicaceae phylogenomics
confirms the complex evolutionary history of the family

J 2025

Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family

DOMINICUS, Lisa J M A; Ihsan A AL-SHEHBAZ; Dmitry A GERMAN; Klaus MUMMENHOFF; Nikolai M HAY et al.

Základní údaje

Originální název

Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family

Autoři

DOMINICUS, Lisa J M A; Ihsan A AL-SHEHBAZ; Dmitry A GERMAN; Klaus MUMMENHOFF; Nikolai M HAY; Martin LYSÁK; Marcus A KOCH; Frederic LENS a Kasper P HENDRIKS

Vydání

Annals of Botany, Oxford, Oxford University Press, 2025, 0305-7364

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10602 Biology , Evolutionary biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.600 v roce 2024

Označené pro přenos do RIV

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1093/aob/mcaf084

UT WoS

001506820400001

Klíčová slova anglicky

Brassicaceae; Cruciferae; mustard family; phylogenomics; mitogenomics; cytonuclear discordance; mitoplastomic discordance; rogue taxa

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 1. 2026 16:52, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Background and Aims: The phylogeny of the Brassicaceae family has traditionally been inferred from plastid and nuclear DNA. However, early studies were limited by the availability of genetic markers and incomplete taxon sampling. Recent phylogenomic studies, leveraging more densely sampled nuclear and plastid datasets, have resolved many taxonomic uncertainties. These studies either targeted complete plastomes or provided extensive representation of the nuclear genome. Nevertheless, substantial cytonuclear discordance, poorly resolved backbone relationships and challenges in placing 'rogue taxa' have left unresolved questions about deeper relationships, notably of the five supertribes of the family. In this context, we performed the first phylogenomic analysis of the slower-evolving, maternally inherited mitogenome, which presents a promising avenue for resolving deeper phylogenetic nodes. Methods: Using published mitogenomes from nine Brassicaceae species, we generated a mitogenomic reference file to recover mitogenomic sequencing read data from Hendriks et al. (2023. Global Brassicaceae phylogeny based on filtering of 1000-gene dataset. Current Biology: CB 33: 4052-4068.e6). Subsequently, we reconstructed a codon-aware mitogenomic supermatrix, alongside updated nuclear (281 genes) and plastome (76 genes) supermatrices and inferred family-wide maximum likelihood phylogenies from each of these three genomes. Congruence among the resulting phylogenies was assessed thoroughly. Key Results: We present the first densely sampled family-wide mitogenomic Brassicaceae phylogeny, including 167 species, 145 genera (40% of the family) and 40 tribes (69% of the family), and the first family-wide phylogenomic comparison based on all three plant genomes. Although cytonuclear discordance was evident, we also uncovered strong phylogenomic discordance between the two organellar genomes (mitogenome and plastome), coined here as 'mitoplastomic discordance'. Our findings offer new insights into the placement of several rogue and previously unplaced taxa. Conclusions: Phylogenomic discordance in Brassicaceae was more pervasive than expected. Although bifurcating phylogenies offer clear evolutionary hypotheses, they do not fully capture evolutionary complexities. Our results have implications for understanding Brassicaceae evolution, taxonomy and systematics, shedding light on processes such as hybridization and genome duplication, commonly resulting in evolutionary reticulation.

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

Citovat

DOMINICUS, Lisa J M A; Ihsan A AL-SHEHBAZ; Dmitry A GERMAN; Klaus MUMMENHOFF; Nikolai M HAY; Martin LYSÁK; Marcus A KOCH; Frederic LENS a Kasper P HENDRIKS. Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family. Annals of Botany. Oxford: Oxford University Press, 2025, 16 s. ISSN 0305-7364. Dostupné z: https://doi.org/10.1093/aob/mcaf084.

@article{2544202,
   author = {Dominicus, Lisa J M A and AlandShehbaz, Ihsan A and German, Dmitry A and Mummenhoff, Klaus and Hay, Nikolai M and Lysák, Martin and Koch, Marcus A and Lens, Frederic and Hendriks, Kasper P},
   article_location = {Oxford},
   doi = {https://doi.org/10.1093/aob/mcaf084},
   keywords = {Brassicaceae; Cruciferae; mustard family; phylogenomics; mitogenomics; cytonuclear discordance; mitoplastomic discordance; rogue taxa},
   language = {eng},
   issn = {0305-7364},
   journal = {Annals of Botany},
   title = {Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family},
   url = {https://doi.org/10.1093/aob/mcaf084},
   year = {2025}
}

TY  - JOUR
ID  - 2544202
AU  - Dominicus, Lisa J M A - Al-Shehbaz, Ihsan A - German, Dmitry A - Mummenhoff, Klaus - Hay, Nikolai M - Lysák, Martin - Koch, Marcus A - Lens, Frederic - Hendriks, Kasper P
PY  - 2025
TI  - Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family
JF  - Annals of Botany
PB  - Oxford University Press
SN  - 03057364
KW  - Brassicaceae
KW  - Cruciferae
KW  - mustard family
KW  - phylogenomics
KW  - mitogenomics
KW  - cytonuclear discordance
KW  - mitoplastomic discordance
KW  - rogue taxa
UR  - https://doi.org/10.1093/aob/mcaf084
N2  - Background and Aims: The phylogeny of the Brassicaceae family has traditionally been inferred from plastid and nuclear DNA. However, early studies were limited by the availability of genetic markers and incomplete taxon sampling. Recent phylogenomic studies, leveraging more densely sampled nuclear and plastid datasets, have resolved many taxonomic uncertainties. These studies either targeted complete plastomes or provided extensive representation of the nuclear genome. Nevertheless, substantial cytonuclear discordance, poorly resolved backbone relationships and challenges in placing 'rogue taxa' have left unresolved questions about deeper relationships, notably of the five supertribes of the family. In this context, we performed the first phylogenomic analysis of the slower-evolving, maternally inherited mitogenome, which presents a promising avenue for resolving deeper phylogenetic nodes. Methods: Using published mitogenomes from nine Brassicaceae species, we generated a mitogenomic reference file to recover mitogenomic sequencing read data from Hendriks et al. (2023. Global Brassicaceae phylogeny based on filtering of 1000-gene dataset. Current Biology: CB 33: 4052-4068.e6). Subsequently, we reconstructed a codon-aware mitogenomic supermatrix, alongside updated nuclear (281 genes) and plastome (76 genes) supermatrices and inferred family-wide maximum likelihood phylogenies from each of these three genomes. Congruence among the resulting phylogenies was assessed thoroughly. Key Results: We present the first densely sampled family-wide mitogenomic Brassicaceae phylogeny, including 167 species, 145 genera (40% of the family) and 40 tribes (69% of the family), and the first family-wide phylogenomic comparison based on all three plant genomes. Although cytonuclear discordance was evident, we also uncovered strong phylogenomic discordance between the two organellar genomes (mitogenome and plastome), coined here as 'mitoplastomic discordance'. Our findings offer new insights into the placement of several rogue and previously unplaced taxa. Conclusions: Phylogenomic discordance in Brassicaceae was more pervasive than expected. Although bifurcating phylogenies offer clear evolutionary hypotheses, they do not fully capture evolutionary complexities. Our results have implications for understanding Brassicaceae evolution, taxonomy and systematics, shedding light on processes such as hybridization and genome duplication, commonly resulting in evolutionary reticulation.
ER  -

DOMINICUS, Lisa J M A; Ihsan A AL-SHEHBAZ; Dmitry A GERMAN; Klaus MUMMENHOFF; Nikolai M HAY; Martin LYSÁK; Marcus A KOCH; Frederic LENS a Kasper P HENDRIKS. Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family. \textit{Annals of Botany}. Oxford: Oxford University Press, 2025, 16 s. ISSN~0305-7364. Dostupné z: https://doi.org/10.1093/aob/mcaf084.

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