Abstract
BACKGROUND: Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood. METHODS: 104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants. RESULTS: We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants. CONCLUSIONS: Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.
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Claims 10
Claim · model-written summary
The 104 SBP-box genes divide into group I and II, and group II further into subgroups II-1 and II-2 by phylogenetic analysis.
- Taxon
- land plantsEmbryophytat0
- Outcome
- divided into group I and IIe0
Not reportedDirection
Verbatim
e0“These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis”
t0“land plants”
Claim · model-written summary
Subgroup II-1 genes have sequence and structural features similar to group I genes.
- Taxon
- land plantsEmbryophytat0
- Gene
- subgroup II-1 genese0
- Outcome
- similar sequence and structural featurese0
Not reportedDirection
Verbatim
e0“subgroup II-1 genes have similar sequence and structural features to group I genes”
t0“land plants”
Claim · model-written summary
Subgroup II-2 genes differ intrinsically on these features, including high copy numbers and miR156/miR529 regulation.
- Taxon
- land plantsEmbryophytat0
- Gene
- subgroup II-2 genese0
- Outcome
- intrinsic differences on these featurese0
- Qualifier
- high copy numbers and the presence of miR156/miR529 regulatione0
Not reportedDirection
Verbatim
e0“subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation”
t0“land plants”
Claim · model-written summary
Subgroup II-1 genes are constrained by stronger purifying selection than subgroup II-2 genes.
Verbatim
e0“subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes”
t0“land plants”
Claim · model-written summary
Subgroup II-1 genes evolve at a lower substitution rate than subgroup II-2 genes.
Verbatim
e0“subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes”
t0“land plants”
Claim · model-written summary
Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets.
Verbatim
e0“miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection”
t0“land plants”
Claim · model-written summary
Among subgroup II-2 genes, miR156 targets experience comparatively relaxed purifying selection relative to miR529 targets.
Verbatim
e0“miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection”
t0“land plants”
Claim · model-written summary
Subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation.
- Taxon
- land plantsEmbryophytat0
- Gene
- subgroup II-2 genese0
- Outcome
- diversifiede0
- Qualifier
- gene copy duplications and changes in miR156/529 regulatione0
Verbatim
e0“subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation”
t0“land plants”
Claim · model-written summary
The authors hypothesize that this diversification might contribute to morphological diversifications of land plants.
- Taxon
- land plantsEmbryophytae0
- Outcome
- morphological diversificationse0
- Qualifier
- might contributee0
Verbatim
e0“which might contribute to morphological diversifications of land plants”
Claim · model-written summary
Different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants.
- Taxon
- land plantsEmbryophytae0
- Gene
- SBP-box genese0
- Outcome
- differing evolutionary patternse0
- Qualifier
- different evolutionary rates and selection strengthse0
Verbatim
e0“different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants”