Data References
Genome sequence and CactusFlyBase annotation can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Pooled RNA-seq for annotation data can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Catalina Island tissue specific RNA-seq can be cited with:
Yang, Haiwang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, and Brian Oliver. "Re-annotation of eight Drosophila genomes." Life science alliance 1, no. 6 (2018). https://doi.org/10.26508/lsa.201800156
Catalina Island RefSeq annotation transfer based version GCF_018153725.1 available here:
https://www.ncbi.nlm.nih.gov/assembly/GCF_018153725.1
O'Leary, Nuala A., Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput et al. "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic acids research 44, no. D1 (2016): D733-D745. https://doi.org/10.1093/nar/gkv1189
Larva brain and body RNA-seq can be cited with:
Benowitz, Kyle M., Joshua M. Coleman, Carson W. Allan, and Luciano M. Matzkin. "Contributions of cis-and trans-regulatory evolution to transcriptomic divergence across populations in the Drosophila mojavensis larval brain." Genome biology and evolution 12, no. 8 (2020): 1407-1418. https://doi.org/10.1093/gbe/evaa145
Genome sequence and CactusFlyBase annotation can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Pooled RNA-seq for annotation data can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Genome sequence and CactusFlyBase annotation can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Pooled RNA-seq for annotation data can be cited with:
Benowitz, Kyle M., Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin "Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila." Genome Biology and Evolution Volume 16, Issue 9 (2024). https://doi.org/10.1093/gbe/evae191
Life stage specific RNA-seq can be cited with:
Vanderlinde, Thyago, Eduardo Guimarães Dupim, Nestor O. Nazario-Yepiz, and Antonio Bernardo Carvalho. "An improved genome assembly for Drosophila navojoa, the basal species in the mojavensis cluster." Journal of Heredity 110, no. 1 (2019): 118-123. https://doi.org/10.1093/jhered/esy059
Genome sequence and 2015 Freeze 1 annotation can be cited with:
Guillén, Yolanda, Núria Rius, Alejandra Delprat, Anna Williford, Francesc Muyas, Marta Puig, Sònia Casillas et al. "Genomics of ecological adaptation in cactophilic Drosophila." Genome biology and evolution 7, no. 1 (2015): 349-366. https://doi.org/10.1093/gbe/evu291
Life stage specific RNA-seq can be cited with:
Guillén, Yolanda, Núria Rius, Alejandra Delprat, Anna Williford, Francesc Muyas, Marta Puig, Sònia Casillas et al. "Genomics of ecological adaptation in cactophilic Drosophila." Genome biology and evolution 7, no. 1 (2015): 349-366. https://doi.org/10.1093/gbe/evu291
Moreyra et al. 2023 annotation can be cited with:
Moreyra, Nicolás Nahuel, Francisca Cunha Almeida, Carson Allan, Nicolás Frankel, Luciano Matías Matzkin, and Esteban Hasson. "Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila." Molecular Phylogenetics and Evolution 178 (2023): 107653. https://doi.org/10.1016/j.ympev.2022.107653
Accessory Gland RNA-seq can be cited with:
Hurtado, J, F Almeida, S Revale, and E Hasson. “Revised Phylogenetic Relationships within the Drosophila Buzzatii Species Cluster (Diptera: Drosophilidae: Drosophila Repleta Group) Using Genomic Data.” Arthropod Systematics and Phylogeny 77 (2019): 239–50. https://doi.org/10.26049/ASP77-2-2019-03
Testes and Ovaries RNA-seq can be cited with:
Romero-Soriano, Valèria, Laurent Modolo, Hélène Lopez-Maestre, Bruno Mugat, Eugénie Pessia, Séverine Chambeyron, Cristina Vieira, and Maria Pilar Garcia Guerreiro. "Transposable element misregulation is linked to the divergence between parental piRNA pathways in Drosophila hybrids." Genome biology and evolution 9, no. 6 (2017): 1450-1470. https://doi.org/10.1093/gbe/evx091
Genome sequence and annotation can be cited with:
Moreyra, Nicolás Nahuel, Francisca Cunha Almeida, Carson Allan, Nicolás Frankel, Luciano Matías Matzkin, and Esteban Hasson. "Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila." Molecular Phylogenetics and Evolution 178 (2023): 107653. https://doi.org/10.1016/j.ympev.2022.107653
Accessory Gland RNA-seq can be cited with:
Hurtado, J, F Almeida, S Revale, and E Hasson. “Revised Phylogenetic Relationships within the Drosophila Buzzatii Species Cluster (Diptera: Drosophilidae: Drosophila Repleta Group) Using Genomic Data.” Arthropod Systematics and Phylogeny 77 (2019): 239–50. https://doi.org/10.26049/ASP77-2-2019-03
Genome sequence and annotation can be cited with:
Moreyra, Nicolás Nahuel, Francisca Cunha Almeida, Carson Allan, Nicolás Frankel, Luciano Matías Matzkin, and Esteban Hasson. "Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila." Molecular Phylogenetics and Evolution 178 (2023): 107653. https://doi.org/10.1016/j.ympev.2022.107653
Accessory Gland RNA-seq can be cited with:
Hurtado, J, F Almeida, S Revale, and E Hasson. “Revised Phylogenetic Relationships within the Drosophila Buzzatii Species Cluster (Diptera: Drosophilidae: Drosophila Repleta Group) Using Genomic Data.” Arthropod Systematics and Phylogeny 77 (2019): 239–50. https://doi.org/10.26049/ASP77-2-2019-03
Genome sequence and annotation for both A and B lines can be cited with:
Moreyra, Nicolás Nahuel, Francisca Cunha Almeida, Carson Allan, Nicolás Frankel, Luciano Matías Matzkin, and Esteban Hasson. "Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila." Molecular Phylogenetics and Evolution 178 (2023): 107653. https://doi.org/10.1016/j.ympev.2022.107653
Accessory Gland RNA-seq can be cited with:
Hurtado, J, F Almeida, S Revale, and E Hasson. “Revised Phylogenetic Relationships within the Drosophila Buzzatii Species Cluster (Diptera: Drosophilidae: Drosophila Repleta Group) Using Genomic Data.” Arthropod Systematics and Phylogeny 77 (2019): 239–50. https://doi.org/10.26049/ASP77-2-2019-03
Genome sequence and annotation can be cited with:
Rane, Rahul V., Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò et al. "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species." BMC genomics 20, no. 1 (2019): 1-22. https://doi.org/10.1186/s12864-018-5413-3
Mixed Life Stage RNA-seq can be cited with:
Rane, Rahul V., Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò et al. "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species." BMC genomics 20, no. 1 (2019): 1-22. https://doi.org/10.1186/s12864-018-5413-3
Genome sequence and annotation can be cited with:
Rane, Rahul V., Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò et al. "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species." BMC genomics 20, no. 1 (2019): 1-22. https://doi.org/10.1186/s12864-018-5413-3
Mixed Life Stage RNA-seq can be cited with:
Rane, Rahul V., Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò et al. "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species." BMC genomics 20, no. 1 (2019): 1-22. https://doi.org/10.1186/s12864-018-5413-3
Genome sequence and annotation can be cited with:
NCBI RefSeq GCF_003285905.1 DhydRS2
O'Leary, Nuala A., Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput et al. "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic acids research 44, no. D1 (2016): D733-D745. https://doi.org/10.1093/nar/gkv1189
Mixed Life Stage RNA-seq can be cited with:
Rane, Rahul V., Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò et al. "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species." BMC genomics 20, no. 1 (2019): 1-22. https://doi.org/10.1186/s12864-018-5413-3
Adult Male and Female RNA-seq can be cited with:
Zhao, Li, and David J. Begun. "Genomics of parallel adaptation at two timescales in Drosophila." PLoS genetics 13, no. 10 (2017): e1007016. https://doi.org/10.1371/journal.pgen.1007016
Drosophila virilis
Genome sequence and annotation can be cited with:
NCBI RefSeq GCF_003285735.1 DvirRS2
O'Leary, Nuala A., Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput et al. "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic acids research 44, no. D1 (2016): D733-D745. https://doi.org/10.1093/nar/gkv1189
Tissue specific RNA-seq can be cited with:
Yang, Haiwang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, and Brian Oliver. "Re-annotation of eight Drosophila genomes." Life science alliance 1, no. 6 (2018). https://doi.org/10.26508/lsa.201800156
Drosophila melanogaster
Genome sequence and annotation can be cited with:
FlyBase Drosophila melanogaster r6.40 (FB2021_03)
Gramates, L. Sian, Julie Agapite, Helen Attrill, Brian R. Calvi, Madeline A. Crosby, Gilberto Dos Santos, Joshua L. Goodman et al. "FlyBase: a guided tour of highlighted features." Genetics 220, no. 4 (2022): iyac035. https://doi.org/10.1093/genetics/iyac035
Hoskins, Roger A., Joseph W. Carlson, Kenneth H. Wan, Soo Park, Ivonne Mendez, Samuel E. Galle, Benjamin W. Booth et al. "The Release 6 reference sequence of the Drosophila melanogaster genome." Genome research 25, no. 3 (2015): 445-458. https://doi.org/10.1101/gr.185579.114
Tissue specific RNA-seq can be cited with:
Yang, Haiwang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, and Brian Oliver. "Re-annotation of eight Drosophila genomes." Life science alliance 1, no. 6 (2018). https://doi.org/10.26508/lsa.201800156
Drosophila grimshawi
Genome sequence and annotation can be cited with:
Drosophila 12 Genomes Consortium. "Evolution of genes and genomes on the Drosophila phylogeny." Nature 450, no. 7167 (2007): 203-218. https://doi.org/10.1038/nature06341
NCBI GenBank GCA_000005155.1 dgri_caf1
O'Leary, Nuala A., Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput et al. "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." Nucleic acids research 44, no. D1 (2016): D733-D745. https://doi.org/10.1093/nar/gkv1189
Tissue specific RNA-seq can be cited with:
Yang, Haiwang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, and Brian Oliver. "Re-annotation of eight Drosophila genomes." Life science alliance 1, no. 6 (2018). https://doi.org/10.26508/lsa.201800156