Additional file 1 of The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
Creators: name: Rispe, Claude
name: Legeai, Fabrice
name: Nabity, Paul D.
name: Fernández, Rosa
name: Arora, Arinder K.
name: Baa-Puyoulet, Patrice
name: Banfill, Celeste R.
name: Bao, Leticia
name: Barberà, Miquel
name: Bouallègue, Maryem
name: Bretaudeau, Anthony
name: Brisson, Jennifer A.
name: Calevro, Federica
name: Capy, Pierre
name: Catrice, Olivier
name: Chertemps, Thomas
name: Couture, Carole
name: Delière, Laurent
name: Douglas, Angela E.
name: Dufault-Thompson, Keith
name: Escuer, Paula
name: Feng, Honglin
name: Forneck, Astrid
name: Gabaldón, Toni
name: Guigó, Roderic
name: Hilliou, Frédérique
name: Hinojosa-Alvarez, Silvia
name: Hsiao, Yi-min
name: Hudaverdian, Sylvie
name: Jacquin-Joly, Emmanuelle
name: James, Edward B.
name: Johnston, Spencer
name: Joubard, Benjamin
name: Le Goff, Gaëlle
name: Le Trionnaire, Gaël
name: Librado, Pablo
name: Liu, Shanlin
name: Lombaert, Eric
name: Lu, Hsiao-ling
name: Maïbèche, Martine
name: Makni, Mohamed
name: Marcet-Houben, Marina
name: Martínez-Torres, David
name: Meslin, Camille
name: Montagné, Nicolas
name: Moran, Nancy A.
name: Papura, Daciana
name: Parisot, Nicolas
name: Rahbé, Yvan
name: Lopes, Mélanie Ribeiro
name: Ripoll-Cladellas, Aida
name: Robin, Stéphanie
name: Roques, Céline
name: Roux, Pascale
name: Rozas, Julio
name: Sánchez-Gracia, Alejandro
name: Sánchez-Herrero, Jose F.
name: Santesmasses, Didac
name: Scatoni, Iris
name: Serre, Rémy-Félix
name: Tang, Ming
name: Tian, Wenhua
name: Umina, Paul A.
name: van Munster, Manuella
name: Vincent-Monégat, Carole
name: Wemmer, Joshua
name: Wilson, Alex C. C.
name: Zhang, Ying
name: Zhao, Chaoyang
name: Zhao, Jing
name: Zhao, Serena
name: Zhou, Xin
name: Delmotte, François
name: Tagu, Denis
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figures. S1-S22, Table S1-S20, Methods and Results. Figure S1. Mitochondrial genome view of grape phylloxera. Figure S2. Proportion of transposable elements (TE) in the genome. Figure S3. GO terms of phylloxera-specific genes. Figure S4. Enriched GO terms in the phylloxera genome with and without TEs. Figure S5. Gene gain/loss at different nodes or branches. Figure S6. Species phylogenetic tree based on insect genomes and the transcriptomes of Planoccoccus citri and Adelges tsugae. Figure S7. Diagram of the gap-filling and annotation process. Figure S8. Urea cycle in D. vitifoliae and A. pisum. Figure S9. IMD immune pathway in D. vitifoliae.Figure S10. Phylogenetic tree of RR-1 cuticular proteins.Figure S11. Phylogenetic tree of RR-2 cuticular proteins.Figure S12. Comparison of miRNAs in D. vitifoliae and other insect genomes. Figure S13. Phylogenetic tree of aquaporin protein sequences. Figure S14. Comparison of the phylloxera PER protein with other insects. Figure S15. Amino acid alignment of PTTH amino acid sequences. Figure S16. Phylogeny of hemipteran ORs. Figure S17. Phylogeny of hemipteran GRs. Figure S18. Phylogenetic analysis of OBPs. Figure S19. Phylogenetic analysis of CSPs. Figure S20. Phylogenetic analysis of NPC2s. Figure S21. Distribution of cluster sizes of putative effectors. Figure S22. Physical distribution of the three largest clusters of effectors. Table S1. Genes of bacterial and fungal origin. Table S2. Statistics on TEs. Table S3. GO enrichment of genes duplicated at different ancestral nodes. Table S4. Metabolic gaps in the D. vitifoliae reaction network. Table S5. Functional annotation of metabolic genes. Table S6. Genes of the TOLL pathway. Table S7. Genes of the IMD pathway. Table S8. Statistics on cuticular proteins. Table S9. Developmental genes in D. vitifoliae and A. pisum. Table S10. miRNAs. Table S11. Clock-related genes. Table S12. List of ORs and GRs. Table S13. Number of OBPs, CSPs and NPC2s. Table S14. List of Cytochromes P450. Table S15. List of genes involved in detoxification. Table S16. Effector genes with predicted domains and their corresponding functions. Table S17. Statistics on sequence reads and SRA accessions used for the reference genome. Table S18. List of species used to study gene expansions. Table S19. Sampling sites and SRA used for population genomics analyses. Table S20. Prior distribution of parameters used for ABC modeling of invasion routes.