Abstract
BACKGROUND: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. RESULTS: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. CONCLUSIONS: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.
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Claims 13
Claim · model-written summary
A chromosome-level Buxus austro-yunnanensis genome was provided.
- Taxon
- Buxus austro-yunnanensisBuxus austroyunnanensise0
- Outcome
- high-quality chromosome-level genomee0
- Value
- chromosome-levele0
Verbatim
e0“we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales).”
Claim · model-written summary
Buxales and Trochodendrales were classified as sister lineages.
- Taxon
- Buxus austro-yunnanensisBuxus austroyunnanensist0
- Outcome
- classified as sisterse0
- Comparator
- Trochodendralese0
Verbatim
e0“Buxales and Trochodendrales are genetically similar and classified as sisters.”
t0“Buxus austro-yunnanensis”
Claim · model-written summary
Buxales and Trochodendrales were placed as sisters to core eudicots.
- Taxon
- Buxus austro-yunnanensisBuxus austroyunnanensist0
- Outcome
- sisters to the core eudicotse0
- Comparator
- core eudicotse0
Verbatim
e0“both are sisters to the core eudicots”
t0“Buxus austro-yunnanensis”
Claim · model-written summary
Ranunculales was the first lineage to diverge from these groups.
- Taxon
- RanunculalesRanunculalese0
- Outcome
- first lineage to divergee0
Verbatim
e0“Ranunculales was found to be the first lineage to diverge from these groups.”
Claim · model-written summary
Incomplete lineage sorting and hybridization were identified as main contributors to 34.33% phylogenetic discordance.
- Taxon
- Buxus austro-yunnanensisBuxus austroyunnanensist0
- Outcome
- phylogenetic discordancee0
- Value
- 34.33%e0
- Qualifier
- Incomplete lineage sorting and hybridizatione0
Verbatim
e0“Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages.”
t0“Buxus austro-yunnanensis”
Claim · model-written summary
B. austro-yunnanensis underwent one whole-genome duplication event.
Verbatim
e0“B. austro-yunnanensis underwent only one whole-genome duplication event”
Claim · model-written summary
Collinear gene phylogenies suggested independent polyploidizations in five eudicot lineages.
Verbatim
e0“separate independent polyploidizations occurred in the five eudicot lineages.”
Claim · model-written summary
The ancestral eudicot karyotype was reconstructed.
Verbatim
e0“we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species.”
Claim · model-written summary
Nearly gapless karyotype projections were generated for each eudicot species.
Verbatim
e0“we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species.”
Claim · model-written summary
A common chromosome fusion event was recovered in asterids.
Verbatim
e0“we recovered one common chromosome fusion event in asterids and malvids, respectively.”
Claim · model-written summary
A common chromosome fusion event was recovered in malvids.
Verbatim
e0“we recovered one common chromosome fusion event in asterids and malvids, respectively.”
Claim · model-written summary
Aquilegia and Vitis fused ancestral karyotypes at different positions.
AquilegiaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions”
Claim · model-written summary
Different fusion positions imply different karyotype evolution histories for Aquilegia and Vitis.
- Taxon
- Buxus austro-yunnanensisBuxus austroyunnanensist0
- Outcome
- different karyotype evolution historiese0
- Qualifier
- differente0
Verbatim
e0“these two species have different karyotype evolution histories.”
t0“Buxus austro-yunnanensis”