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

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.

本论文的在线补充表格源自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.等学者2017年发表于《国际寄生虫学杂志》（已付印）的研究论文，论文题为《牛蜱（Rhipicephalus microplus）的基因富集草图基因组：结合PacBio（Pacific Biosciences）与Illumina测序技术的混合组装策略实现高重复度基因组分析》。

补充表S5：牛蜱（Rhipicephalus microplus）Rmi v2.0基因组组装中各鉴定基因座的代表序列功能注释。本次注释包含核苷酸与蛋白质序列、AutoFACT基因描述结果、BUSCO节肢动物祖先蛋白质评估结果与E值，同时附带KEGG（Kyoto Encyclopedia of Genes and Genomes，京都基因与基因组百科全书）通路、COG（Clusters of Orthologous Groups，直系同源基因簇）与GO（Gene Ontology，基因本体）注释信息。

补充表S7：与BUSCO分析中缺失的节肢动物祖先基因序列具有相似性的转录本定位及候选基因座预测。本次展示了BUSCO分析中1603个缺失祖先蛋白质的部分候选基因座子集，同时展示了在Rmi v2.0基因组组装中无比对结果的BUSCO节肢动物祖先蛋白质。

补充表S8：牛蜱（Rhipicephalus microplus）“gag-pol融合蛋白”与最近缘参考比对序列的BLASTP序列比对结果（AutoFACT注释及序列相似性结果详见补充表S5）。

补充表S9：Rmi_v1.0、Rmi_v2.0与肩突硬蜱（Ixodes scapularis）IscaW1蛋白质的GO（Gene Ontology，基因本体）注释对比。所有蛋白质集均通过AutoFACT完成注释，随后使用WEGO（http://wego.genomics.org.cn/）进行比对分析。相较于IscaW1，牛蜱Rmi_v2.0基因组组装中上调幅度≥4倍的GO分类条目，在“细胞组分”“分子功能”与“生物过程”三大类别下均以绿色背景高亮显示。

补充表S10：牛蜱与肩突硬蜱之间GO差异最显著的基因/蛋白质的GO注释（详细信息详见补充表S9）。

补充表S11：Rmi v2.0基因组组装中预测得到的牛蜱（Rhipicephalus microplus）微小RNA（miRNA，microRNA）。

补充表S12：OrthoMCL分析结果，展示牛蜱、肩突硬蜱各自特有以及二者共有的蛋白质家族与蛋白质。具体包括：牛蜱特有的蛋白质家族（蛋白质簇）；牛蜱与肩突硬蜱共有的蛋白质家族（蛋白质簇）：各蛋白质簇对应的Rmi v2.0基因座登录号；牛蜱与肩突硬蜱共有的蛋白质家族（蛋白质簇）：各蛋白质簇对应的Isca W1基因登录号；以及肩突硬蜱特有的蛋白质家族（蛋白质簇）。