Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae)
Abstract
:1. Introduction
2. Results
2.1. Ten New Transcriptomes for Arundo and Arundinoideae Taxa
2.2. A Nuclear Phylogenomic Reconstruction of Arundo Species Reveals A. Formosana as Basal and A. Micrantha as Likely Hybrid
2.3. Extended Plastidial Dataset Confirms Basal A. Formosana and Supports Parphyletic A. Donax
2.4. Molecular Dating of Arundo Origin
2.5. Demiduplication Is the Most Prominent Mechanism of Chromosome Number Evolution in Arundo
2.6. Patterns of Molecular Evolution Identify Candidate Genes under Positive Selection in Arundo and Arundinoideae
3. Discussion
3.1. A New Scenario of Arundo Phylogeny
3.2. Hybridization Events Clarified
3.3. Recurrent Demipolyploidization in the Arundo Genus Does Not Lead to Tetraplodization
3.4. Implications for Genetic Improvement in Arundo
4. Materials and Methods
4.1. Transcriptome de Novo Assembly
4.2. Gene Functional Annotation
4.3. Orthologous Groups Identification and Supermatrix Construction
4.4. Phylogenomic Reconstruction of Arundo Species with Nuclear Genes
4.5. Phylogenetic Reconstruction of Arundinoideae Using the Plastidial Dataset
4.6. Molecular Dating
4.7. Inference of Chromosome-Number Change
4.8. Molecular Evolution Analyses
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
MYA | Million years ago |
GO | Gene ontology |
ML | Maxim likelihood |
MP | Maxim parsimony |
BI | Bayesian inference |
gCF | Gene concordance factor |
sCF | Site concordance factor |
gEF_p | Probability of equal frequencies rejection for genes |
sEF_p | Probability of equal frequencies rejection for genes |
gIC | Gene Internode Certainty |
sIC | Site Internode Certainty |
PP | Posterior probability |
UFBOOT | Ultrafast bootstrap |
npBS | Nonparametric bootstrap |
HPD | High Posterior Densities |
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MODEL | Parameters | Ln(Likelihood) | AIC | ΔAIC |
---|---|---|---|---|
CONST_RATE_DEMI_EST * | 4 | −14.92 | 37.83 | 0.00 |
CONST_RATE_DEMI | 3 | −17.83 | 41.67 | 3.83 |
BASE_NUM | 4 | −20.30 | 48.61 | 10.77 |
BASE_NUM_DUPL | 5 | −20.18 | 50.36 | 12.53 |
CONST_RATE | 3 | −29.81 | 65.61 | 27.78 |
CONST_RATE_NO_DUPL | 2 | −31.15 | 66.30 | 28.47 |
LINEAR_RATE_DEMI | 5 | −29.61 | 69.22 | 31.39 |
LINEAR_RATE | 5 | −29.99 | 69.98 | 32.14 |
LINEAR_RATE_NO_DUPL | 4 | −31.02 | 70.03 | 32.20 |
LINEAR_RATE_DEMI_EST | 6 | −29.49 | 70.98 | 33.14 |
OG ID | Sites | LR | p-Value | Fdr | TAIR_ID | Name | Description |
---|---|---|---|---|---|---|---|
OG0018377 | 1531 | 39.72 | 2.38 × 10−9 | 2.88 × 10−7 | AT5G47690 | PDS5A | PO76/PDS5 cohesin cofactor |
OG0018357 | 964 | 29.35 | 4.23 × 10−7 | 3.05 × 10−5 | AT4G34100 | CER9 | RING/U-box-superfamily-protein |
OG0018102 | 258 | 22.17 | 1.53 × 10−5 | 0.000735 | AT5G48300 | ADG1 | ADP glucose pyrophosphorylase 1 |
OG0018342 | 973 | 17.99 | 0.000124 | 0.004471 | AT4G11420 | EIF3A | Eukaryotic translation initiation factor 3 subunit A |
OG0018364 | 899 | 13.89 | 0.000965 | 0.027788 | AT4G16150 | CAMTA5 | Calmodulin-binding; transcription-regulators |
OG0018157 | 445 | 12.44 | 0.001986 | 0.047669 | AT4G35140 | NA | Transducin/WD40-repeat-like-superfamily-protein |
OG0018070 | 126 | 12.10 | 0.002359 | 0.048518 | NA | NA | NA |
OG ID | Test Nodes | K | LR | FDR p-Val a | TAIR ID | Name | Description |
---|---|---|---|---|---|---|---|
OG0017620 | hm | 4.35 | 6.19 | 0.030 | AT5G19210 | NA | P-loop containing nucleoside triphosphate hydrolases superfamily protein |
OG0018017 | ami | 3.69 | 10.02 | 0.014 | AT1G64710 | NA | GroES-like zinc-binding alcohol dehydrogenase family protein |
OG0018069 | adf | 39.10 | 8.39 | 0.014 | AT5G42020 | BIP2 | Luminal binding protein involved in polar nuclei fusion during proliferation of endosperm nuclei. |
OG0018170 | pa | 3.79 | 9.98 | 0.009 | AT2G01680 | NA | Ankyrin repeat family protein |
OG0018204 | adf | 4.73 | 6.09 | 0.028 | AT5G08530 | CI51 | 51 kDa subunit of mitochondrial complex I |
OG0018205 | mc | 9.25 | 15.13 | 0 | AT3G15140 | ERI-1 | Ribonuclease H-like superfamily functioning as siRNA exonuclease. It affects post-transcriptional gene silencing and growth rate /biomass. |
OG0018357 * | ama, mc | 3.67 | 7.93 | 0.014 | AT4G34100 | CER9 | Involved in cuticular wax biosynthesis. Arabidopsis mutants have leaf waxes nearly pure C24 and C26 acid, weakly glaucous stem surface, and reduced fertility in early flowers. |
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Jike, W.; Li, M.; Zadra, N.; Barbaro, E.; Sablok, G.; Bertorelle, G.; Rota-Stabelli, O.; Varotto, C. Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae). Int. J. Mol. Sci. 2020, 21, 5247. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155247
Jike W, Li M, Zadra N, Barbaro E, Sablok G, Bertorelle G, Rota-Stabelli O, Varotto C. Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae). International Journal of Molecular Sciences. 2020; 21(15):5247. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155247
Chicago/Turabian StyleJike, Wuhe, Mingai Li, Nicola Zadra, Enrico Barbaro, Gaurav Sablok, Giorgio Bertorelle, Omar Rota-Stabelli, and Claudio Varotto. 2020. "Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae)" International Journal of Molecular Sciences 21, no. 15: 5247. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155247