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1. Additional file 5 of Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Author

Savini, Grazia, Scolari, Francesca, Ometto, Lino, Rota-Stabelli, Omar, Carraretto, Davide, Gomulski, Ludvik M., Gasperi, Giuliano, Abd-Alla, Adly M. M., Aksoy, Serap, Attardo, Geoffrey M., and Malacrida, Anna R.

Abstract

Additional file 5: Table S5. Number of MAG genes (n = 10) in G. m. morsitans, G. austeni, G. fuscipes, G. pallidipes and G. palpalis tested for positive selection after site (A and B), branch (Br) and branch-site (BrS) models. Dataset column indicates the number of species in which ortholog sequences of each G. m. morsitans gene were identified (b = G. brevipalpis; ppi = G. palpalis). Gene ID column reports G. m. morsitans orthologs. NTP indicate genes encoding Novel Tsetse Proteins. * FDR

Published
2021
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2. Additional file 6 of Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Author

Savini, Grazia, Scolari, Francesca, Ometto, Lino, Rota-Stabelli, Omar, Carraretto, Davide, Gomulski, Ludvik M., Gasperi, Giuliano, Abd-Alla, Adly M. M., Aksoy, Serap, Attardo, Geoffrey M., and Malacrida, Anna R.

Abstract

Additional file 6: Table S6. List of species, strains and genome resources used in this study.

Published
2021
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3. Additional file 4 of Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Author

Savini, Grazia, Scolari, Francesca, Ometto, Lino, Rota-Stabelli, Omar, Carraretto, Davide, Gomulski, Ludvik M., Gasperi, Giuliano, Abd-Alla, Adly M. M., Aksoy, Serap, Attardo, Geoffrey M., and Malacrida, Anna R.

Abstract

Additional file 4: Table S4. Testes genes (n = 176) in G. m. morsitans, G. austeni, G. fuscipes, G. pallidipes and G. palpalis tested for positive selection after site (A and B), branch (Br) and branch-site (BrS) models. Dataset column indicates the number of species in which ortholog sequences of each G. m. morsitans gene were identified (aus = G. austeni; b = G. brevipalpis; f = G. fuscipes; pai = G. pallidipes; ppi = G. palpalis). Gene ID column reports G. m. morsitans orthologs. NTP indicate genes encoding Novel Tsetse Proteins. * FDR

Published
2021
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5. Additional file 4 of Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

Author

Carraretto, Davide, Nidchaya Aketarawong, Cosimo, Alessandro Di, Manni, Mosè, Scolari, Francesca, Valerio, Federica, Malacrida, Anna R., Gomulski, Ludvik M., and Gasperi, Giuliano

Subjects
mental disorders
Abstract

Additional file 4: Figure S3. Sequence of the extended contig3 showing the positions of an exon (yellow rectangle) and primers.

Published
2020
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7. Additional file 3 of Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

Author

Carraretto, Davide, Nidchaya Aketarawong, Cosimo, Alessandro Di, Manni, Mosè, Scolari, Francesca, Valerio, Federica, Malacrida, Anna R., Gomulski, Ludvik M., and Gasperi, Giuliano

Subjects
mental disorders
Abstract

Additional file 3: Figure S2. Sequence of the extended contig2 showing the positions exons (yellow rectangles) and primers.

Published
2020
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8. Additional file 7 of Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

Author

Carraretto, Davide, Nidchaya Aketarawong, Cosimo, Alessandro Di, Manni, Mosè, Scolari, Francesca, Valerio, Federica, Malacrida, Anna R., Gomulski, Ludvik M., and Gasperi, Giuliano

Abstract

Additional file 7: Figure S6. Alignment of part of the extended contig2 and Scaffold01347 (NW_011875054.1), indicating the positions of primers designed to amplify preferentially the NW_011875054.1 sequence.

Published
2020
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9. Additional file 2 of Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

Author

Carraretto, Davide, Nidchaya Aketarawong, Cosimo, Alessandro Di, Manni, Mosè, Scolari, Francesca, Valerio, Federica, Malacrida, Anna R., Gomulski, Ludvik M., and Gasperi, Giuliano

Abstract

Additional file 2: Figure S1. Sequence of the extended contig1 showing the positions of the primers. The grey box indicates the extent of the first repetition unit.

Published
2020
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11. Additional file 6 of Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

Author

Carraretto, Davide, Nidchaya Aketarawong, Cosimo, Alessandro Di, Manni, Mosè, Scolari, Francesca, Valerio, Federica, Malacrida, Anna R., Gomulski, Ludvik M., and Gasperi, Giuliano

Subjects
mental disorders
Abstract

Additional file 6.Figure S5. Sequence of the extended contig4 showing the positions of a putative exon (yellow rectangle) and primers.

Published
2020
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12. Additional file 13: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author

Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Aurélie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap

Abstract

Review history. (DOCX 31 kb)

Published
2019
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13. Additional file 1: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author

Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Aurélie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap

Abstract

Supplementary text and supplementary tables. (DOCX 186 kb)

Published
2019
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14. Additional file 3: of The Nix locus on the male-specific homologue of chromosome 1 in Aedes albopictus is a strong candidate for a male-determining factor

Author

Gomulski, Ludvik, Mariconti, Marina, Cosimo, Alessandro Di, Scolari, Francesca, Mosè Manni, Savini, Grazia, Malacrida, Anna, and Gasperi, Giuliano

Subjects
body regions, nervous system, mental disorders, fungi, psychological phenomena and processes
Abstract

Figure S1. (PDF) Sequence of the Nix locus showing the positions of the exons (green box), intron and predicted amino acid sequence. The positions of the primers are shown. (PDF 76 kb)

Published
2018
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16. Additional file 4: of Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans

Author

Scolari, Francesca, Attardo, Geoffrey, Aksoy, Emre, Weiss, Brian, Savini, Grazia, Takac, Peter, Adly Abd-Alla, Parker, Andrew, Aksoy, Serap, and Malacrida, Anna

Abstract

Gene Ontology analysis of genes down-regulated in GmmApo male reproductive tissues. The number of genes associated with corresponding Gene Ontology terms (Biological Process, Molecular Function, and Cellular Component Level III) is shown. (PDF 784Â kb)

Published
2018
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17. Additional file 7: of Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans

Author

Scolari, Francesca, Attardo, Geoffrey, Aksoy, Emre, Weiss, Brian, Savini, Grazia, Takac, Peter, Adly Abd-Alla, Parker, Andrew, Aksoy, Serap, and Malacrida, Anna

Subjects
nervous system, sense organs, skin and connective tissue diseases
Abstract

Changes in transcript abundance in response to maturation and mating in the presence of symbionts of genes down- and up-regulated in GmmApo male reproductive tissues. Fold change difference in expression is separately shown for MAG- and testes-biased genes for A) GmmApo down-regulated, and B) GmmApo up-regulated genes. (PDF 893Â kb)

Published
2018
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19. Additional file 4: of The Nix locus on the male-specific homologue of chromosome 1 in Aedes albopictus is a strong candidate for a male-determining factor

Author

Gomulski, Ludvik, Mariconti, Marina, Cosimo, Alessandro Di, Scolari, Francesca, Mosè Manni, Savini, Grazia, Malacrida, Anna, and Gasperi, Giuliano

Subjects
body regions, nervous system, fungi
Abstract

Figure S2. (PDF) Alignment of the 12-24 h embryo-derived Nix transcript sequences showing a transcript with intron retention (unspliced) and a spliced transcript. The predicted translation products of the fragments are shown. (PDF 35 kb)

Published
2018
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20. Additional file 5: of Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans

Author

Scolari, Francesca, Attardo, Geoffrey, Aksoy, Emre, Weiss, Brian, Savini, Grazia, Takac, Peter, Adly Abd-Alla, Parker, Andrew, Aksoy, Serap, and Malacrida, Anna

Abstract

Gene Ontology analysis of genes up-regulated in GmmApo male reproductive tissues. The number of genes associated with corresponding Gene Ontology terms (Biological Process, Molecular Function, and Cellular Component Level III) is shown. (PDF 778Â kb)

Published
2018
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21. Additional file 5: of The Nix locus on the male-specific homologue of chromosome 1 in Aedes albopictus is a strong candidate for a male-determining factor

Author

Gomulski, Ludvik, Mariconti, Marina, Cosimo, Alessandro Di, Scolari, Francesca, Mosè Manni, Savini, Grazia, Malacrida, Anna, and Gasperi, Giuliano

Abstract

Figure S3. (PDF) Alignment of the 833 bp Nix fragment from the Rimini reference sequence with the 10 Nix-833r/f PCR product sequences from individuals from four wild population samples (Guangzhou, Arco, Ban Rai, and Velika Gorica) and one sequence from the Chiang Mai pool. Dashes represent missing data and dots indicate identity to the reference sequence. (PDF 144 kb)

Published
2018
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22. Additional file 3: of The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Author

Papanicolaou, Alexie, Schetelig, Marc, Arensburger, Peter, Atkinson, Peter, Benoit, Joshua, Bourtzis, Kostas, Castañera, Pedro, Cavanaugh, John, Hsu Chao, Childers, Christopher, Curril, Ingrid, Dinh, Huyen, HarshaVardhan Doddapaneni, Dolan, Amanda, Dugan, Shannon, Friedrich, Markus, Gasperi, Giuliano, Geib, Scott, Georgakilas, Georgios, Gibbs, Richard, Giers, Sarah, Gomulski, Ludvik, González-Guzmán, Miguel, Guillem-Amat, Ana, Han, Yi, Hatzigeorgiou, Artemis, Hernández-Crespo, Pedro, Hughes, Daniel, Jones, Jeffery, Karagkouni, Dimitra, Koskinioti, Panagiota, Lee, Sandra, Malacrida, Anna, Manni, Mosè, Mathiopoulos, Kostas, Meccariello, Angela, Shwetha Murali, Murphy, Terence, Muzny, Donna, Oberhofer, Georg, Ortego, Félix, Paraskevopoulou, Maria, Poelchau, Monica, Jiaxin Qu, Reczko, Martin, Robertson, Hugh, Rosendale, Andrew, Rosselot, Andrew, Saccone, Giuseppe, Salvemini, Marco, Savini, Grazia, Schreiner, Patrick, Scolari, Francesca, Siciliano, Paolo, Sheina Sim, Tsiamis, George, Ureña, Enric, Vlachos, Ioannis, Werren, John, Wimmer, Ernst, Worley, Kim, Zacharopoulou, Antigone, Richards, Stephen, and Handler, Alfred

Abstract

Supplementary figures S1–S9. Figure S1 Odorant-binding protein (OBP) genes phylogenetic tree. Figure S2 Ionotrophic receptor (IR) genes phylogenetic tree. Figure S3 Opsin genes phylogenetic tree. Figure S4 CYP gene clusters A and B. Figure S5 Glutathione S-transferase genes phylogenetic tree. Figure S6 cysLGIC genes superfamily phylogenetic tree. Figure S7 Cuticle protein gene clusters. Figure S8 CPLCA cuticle protein genes phylogenetic tree. Figure S9 Seminal fluid protein functional classes. (PDF 9425 kb)

Published
2016
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23. Additional file 1: of The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Author

Papanicolaou, Alexie, Schetelig, Marc, Arensburger, Peter, Atkinson, Peter, Benoit, Joshua, Bourtzis, Kostas, Castañera, Pedro, Cavanaugh, John, Hsu Chao, Childers, Christopher, Curril, Ingrid, Dinh, Huyen, HarshaVardhan Doddapaneni, Dolan, Amanda, Dugan, Shannon, Friedrich, Markus, Gasperi, Giuliano, Geib, Scott, Georgakilas, Georgios, Gibbs, Richard, Giers, Sarah, Gomulski, Ludvik, González-Guzmán, Miguel, Guillem-Amat, Ana, Han, Yi, Hatzigeorgiou, Artemis, Hernández-Crespo, Pedro, Hughes, Daniel, Jones, Jeffery, Karagkouni, Dimitra, Koskinioti, Panagiota, Lee, Sandra, Malacrida, Anna, Manni, Mosè, Mathiopoulos, Kostas, Meccariello, Angela, Shwetha Murali, Murphy, Terence, Muzny, Donna, Oberhofer, Georg, Ortego, Félix, Paraskevopoulou, Maria, Poelchau, Monica, Jiaxin Qu, Reczko, Martin, Robertson, Hugh, Rosendale, Andrew, Rosselot, Andrew, Saccone, Giuseppe, Salvemini, Marco, Savini, Grazia, Schreiner, Patrick, Scolari, Francesca, Siciliano, Paolo, Sheina Sim, Tsiamis, George, Ureña, Enric, Vlachos, Ioannis, Werren, John, Wimmer, Ernst, Worley, Kim, Zacharopoulou, Antigone, Richards, Stephen, and Handler, Alfred

Abstract

Supplementary material A. C. capitata genome sequencing approaches, B. Automated annotations, C. Detection of bacterial sequence contamination and D. Screening the C. capitata genome sequence for potential horizontal gene transfer events. (DOCX 601 kb)

Published
2016
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24. Additional file 4: of The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Author

Papanicolaou, Alexie, Schetelig, Marc, Arensburger, Peter, Atkinson, Peter, Benoit, Joshua, Bourtzis, Kostas, Castañera, Pedro, Cavanaugh, John, Hsu Chao, Childers, Christopher, Curril, Ingrid, Dinh, Huyen, HarshaVardhan Doddapaneni, Dolan, Amanda, Dugan, Shannon, Friedrich, Markus, Gasperi, Giuliano, Geib, Scott, Georgakilas, Georgios, Gibbs, Richard, Giers, Sarah, Gomulski, Ludvik, González-Guzmán, Miguel, Guillem-Amat, Ana, Han, Yi, Hatzigeorgiou, Artemis, Hernández-Crespo, Pedro, Hughes, Daniel, Jones, Jeffery, Karagkouni, Dimitra, Koskinioti, Panagiota, Lee, Sandra, Malacrida, Anna, Manni, Mosè, Mathiopoulos, Kostas, Meccariello, Angela, Shwetha Murali, Murphy, Terence, Muzny, Donna, Oberhofer, Georg, Ortego, Félix, Paraskevopoulou, Maria, Poelchau, Monica, Jiaxin Qu, Reczko, Martin, Robertson, Hugh, Rosendale, Andrew, Rosselot, Andrew, Saccone, Giuseppe, Salvemini, Marco, Savini, Grazia, Schreiner, Patrick, Scolari, Francesca, Siciliano, Paolo, Sheina Sim, Tsiamis, George, Ureña, Enric, Vlachos, Ioannis, Werren, John, Wimmer, Ernst, Worley, Kim, Zacharopoulou, Antigone, Richards, Stephen, and Handler, Alfred

Abstract

Supplementary material: C. capitata chemoreceptor genes. (DOCX 194 kb)

Published
2016
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25. Additional file 1: of New Highly Active Antiretroviral drugs and generic drugs for the treatment of HIV infection: a budget impact analysis on the Italian National Health Service (Lombardy Region, Northern Italy)

Author

Restelli, Umberto, Scolari, Francesca, Bonfanti, Paolo, Croce, Davide, and Rizzardini, Giuliano

Abstract

Patientâ s distribution in the second semester of each year of the base case scenario and of the â new and generic drugsâ scenario. (DOCX 39 kb)

Published
2015
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26. Additional file 1: of Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans

Author

Scolari, Francesca, Attardo, Geoffrey, Aksoy, Emre, Weiss, Brian, Savini, Grazia, Takac, Peter, Adly Abd-Alla, Parker, Andrew, Aksoy, Serap, and Malacrida, Anna

Subjects
fungi, bacteria, 3. Good health
Abstract

The effect of tetracycline treatment on the maternal transmission of tsetse endosymbionts. PCR assays on genomic DNA showing that GmmWT flies were positive for Wigglesworthia (Wig Thic), Sodalis (Sod SsaC) and Wolbachia (Wol GroEL), whereas offspring resulting from tetracycline-treated flies lack all three symbionts. The bottom panel shows the amplification of tsetse tubulin beta-1 gene on all samples. A and B lanes represent two PCR replicates performed on pooled genomic DNA from ten males and ten females extracted either at 2 and 8 days post-emergence. (PDF 1070Â kb)

27. Additional file 1: of Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans

Author

Scolari, Francesca, Attardo, Geoffrey, Aksoy, Emre, Weiss, Brian, Savini, Grazia, Takac, Peter, Adly Abd-Alla, Parker, Andrew, Aksoy, Serap, and Malacrida, Anna

Subjects
fungi, bacteria, 3. Good health
Abstract

The effect of tetracycline treatment on the maternal transmission of tsetse endosymbionts. PCR assays on genomic DNA showing that GmmWT flies were positive for Wigglesworthia (Wig Thic), Sodalis (Sod SsaC) and Wolbachia (Wol GroEL), whereas offspring resulting from tetracycline-treated flies lack all three symbionts. The bottom panel shows the amplification of tsetse tubulin beta-1 gene on all samples. A and B lanes represent two PCR replicates performed on pooled genomic DNA from ten males and ten females extracted either at 2 and 8 days post-emergence. (PDF 1070Â kb)

28. Additional file 2: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author

Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Aurélie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap

Subjects
3. Good health
Abstract

Supplemental Figures S1-S12 and associated captions. (PDF 2260 kb)

29. Additional file 2: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author

Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Aurélie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap

Subjects
3. Good health
Abstract

Supplemental Figures S1-S12 and associated captions. (PDF 2260 kb)

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