A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
Abstract
:1. Introduction
2. Materials and Methods
2.1. Probe Sets
2.1.1. Cactaceae120
2.1.2. Angiosperms353
2.2. Bioinformatic Evaluation
2.3. Phylogenetic Reconstruction
2.4. Experimental Evaluation
3. Results
3.1. Cactaceae120 Loci
3.2. Angiosperms353
3.3. Phylogenetic Results
3.4. Experimental Evaluation
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Clade | NCBI SRA # |
---|---|---|
Anacampseros kurtzii | Outgroup | SRR6435355 (Bioproject: PRJNA428216) |
Ariocarpus retusus | Cactoideae | SRR7905834 |
Astrophytum myriostigma | Cactoideae | SRR7905836 |
Carnegiea gigantea | Cactoideae | SRR5036296 |
Copiapoa desertorum | Cactoideae | SRR7905838 (Bioproject: PRJNA493215) |
Coryphantha maiz tablasensis | Cactoideae | SRR7905839 (Bioproject: PRJNA493215) |
Echinocereus pectinatus | Cactoideae | SRR1698109 (Bioproject: PRJNA269655) |
Echinopsis aurea | Cactoideae | SRR7905840 (Bioproject: PRJNA493215) |
Eriosyce wagenknechtii | Cactoideae | SRR7905831 (Bioproject: PRJNA493215) |
Ferocactus latispinus | Cactoideae | SRR7905830 (Bioproject: PRJNA493215) |
Grusonia bradtiana | Opuntioideae | SRR7905852 (Bioproject: PRJNA493215) |
Gymnocalycium mihanovichii | Cactoideae | SRR7905853 (Bioproject: PRJNA493215) |
Hylocereus undatus | Cactoideae | SRR11603181 |
Leuenbergeria bleo | Leuenbergeria + Pereskia | SRR1698112 |
Leuenbergeria guamacho | Leuenbergeria + Pereskia | SRR7905854 (Bioproject: PRJNA493215) |
Maihuenia poeppigii | Maihuenia | SRR7905849 (Bioproject: PRJNA493215) |
Maihueniopsis conoidea | Opuntioideae | SRR7905848 (Bioproject: PRJNA493215) |
Matucana aurantiaca | Cactoideae | SRR7905855 (Bioproject: PRJNA493215) |
Opuntia arenaria | Opuntioideae | SRR7905850 (Bioproject: PRJNA493215) |
O. cochenillifera | Opuntioideae | SRR1698108 |
O. ficus indica | Opuntioideae | SRR3567682 |
O. streptacantha | Opuntioideae | SRR3478181 |
Pachycereus gatesii | Cactoideae | SRR7905847 (Bioproject: PRJNA493215) |
Peniocereus cuixmalensis | Cactoideae | SRR7905861 (Bioproject: PRJNA493215) |
Pereskia grandifolia | Leuenbergeria + Pereskia | SRR1698106 |
Portulaca oleracea 1 | Outgroup | SRR10247085 |
P. oleracea 2 | Outgroup | SRR10247116 |
Pterocactus tuberosus | Opuntioideae | SRR7905860 (Bioproject: PRJNA493215) |
Rhipsalis baccifera | Cactoideae | SRR7905851 (Bioproject: PRJNA493215) |
Salmiopuntia salmiana | Opuntioideae | SRR7905862 (Bioproject: PRJNA493215) |
Stenocereus yunckeri | Cactoideae | SRR7905856 (Bioproject: PRJNA493215) |
Stetsonia coryne | Cactoideae | SRR7905865(Bioproject: PRJNA493215) |
Tacinga lilae | Opuntioideae | SRR7905864 (Bioproject: PRJNA493215) |
Talinopsis frutescens | Outgroup | SRR6435354 (Bioproject: PRJNA428216) |
Tephrocactus bonnieae | Opuntioideae | SRR7905863 (Bioproject: PRJNA493215) |
Tunilla corrugata | Opuntioideae | SRR7905866 (Bioproject: PRJNA493215) |
Angiosperms353 | ||||||
---|---|---|---|---|---|---|
Cactoideae | Leuenbergeria + Pereskia | Maihuenia | Opuntioideae | Outgroup | ||
Cactaceae120 | Cactoideae | 303 120 | 272 | 252 | 288 | 288 |
Leuenbergeria + Pereskia | 109 | 273 109 | 246 | 267 | 269 | |
Maihuenia | 92 | 91 | 254 92 | 249 | 253 | |
Opuntioideae | 119 | 109 | 92 | 295 119 | 281 | |
Outgroup | 117 | 108 | 92 | 116 | 292 117 |
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Acha, S.; Majure, L.C. A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes 2022, 13, 350. https://doi.org/10.3390/genes13020350
Acha S, Majure LC. A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes. 2022; 13(2):350. https://doi.org/10.3390/genes13020350
Chicago/Turabian StyleAcha, Serena, and Lucas C. Majure. 2022. "A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae" Genes 13, no. 2: 350. https://doi.org/10.3390/genes13020350
APA StyleAcha, S., & Majure, L. C. (2022). A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes, 13(2), 350. https://doi.org/10.3390/genes13020350