Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome

Published: 6 June 2017| Version 2 | DOI: 10.17632/s7jrdzfmb7.2
Contributors:
Roberto Barrero,
Felix Guerrero,
Michael Black,
John McCooke,
Brett Chapman,
Faye Schilkey,
Adalberto Perez de Leon,
Sara Bruns,
Jason Dobrye,
Galina Mikhaylenko,
Keith Stormo,
Callum Bell,
Quanzhou Tao,
Robert Bogden,
Paula Moolhuijzen,
Adam Hunter,
Matthew Bellgard

Description

Online Supplementary Tables for the manuscript: Barrero,R.A., Guerrero,F.D., Black,M., McCooke,J., Chapman,B., Schilkey,F., Pérez de León,A.A., Miller,R.J., Bruns,S., Dobry,J., Mikhaylenko,G., Stormo,K., Bell,C., Tao,Q., Bogden,R., Moolhuijzen,P.M., Hunter,A., Bellgard, M.I., 2017. Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome. International Journal of Parasitology (in press). Supplementary Table S5. Functional annotation of representative sequences for each gene loci identified in the cattle tick Rhipicephalus microplus Rmi v2.0 genome assembly. Nucleotide and protein sequences, AutoFACT gene description, BUSCO ancestral arthropod protein assessment and E-value are given, along with KEGG pathway, COG and GO annotation. Supplementary Table S7. Mapping of transcripts and/or prediction of putative gene loci of sequences with similarity to missing BUSCO ancestral artropods genes. Putative partial gene loci are shown for a subset of the 1,603 missing ancestral proteins in the BUSCO analysis. BUSCO ancestral arthropods proteins with no hits in the Rmi v2.0 genome assembly are shown. Supplementary Table S8. BLASTP sequence comparison of Rhipicephalus microplus 'gag-pol fusion proteins' against their closest reference hit (see Supplementary Table S5 for AutoFACT annotation including sequence similarity results). Supplementary Table S9. Comparison of Gene Ontology (GO) annotation between Rmi_v1.0, Rmi_v2.0 and Ixodes scapularis IscaW1 proteins. Proteins from each set were annotated using AutoFACT and then compared using WEGO (http://wego.genomics.org.cn/). GO categories with >= four-fold increase in Rhipicephalus microplus Rmi_v2.0 genome assembly as compared to IscaW1 are highlighted in green background for 'Cellular component', 'Molecular function' and 'Biological process'. Supplementary Table S10. Gene Ontology (GO) annotation for genes/proteins with top GO differences between Rhipicephalus microplus and Ixodes scapularis (see Supplementary Table S9 for details). Supplementary Table S11. Predicted Rhipicephalus microplus microRNAs (miRNAs) in the Rmi v2.0 genome assembly. Supplementary Table S12. OrthoMCL Analysis, showing Protein Families and Proteins Unique to Rhipicephalus microplus, Ixodes scapularis, or both. Protein families (protein clusters) unique to R. microplus. Protein families (protein clusters) unique to both R. microplus and I. scapularis ticks: Rmi v2.0 gene loci accessions for each protein cluster. Protein families (protein clusters) unique to both R. microplus and I. scapularis ticks: Isca W1 gene accessions for each protein cluster. Protein familes (protein clusters) unique to I. scapularis.

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