Additional file 2 of De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

Additional file 2: Table S1. Sequencing libraries used, sequence results, and kmer optimization for the GCA_001188975.2 assembly. Table S2. Comparison of assembly quality of the 3 main assemblies. Table S3. Assembly statistics for 9 different assemblies generated. Table S4. Comparison of assembly quality of the 3 Y chromosome assemblies. Table S5. Sequences of the primers used for the validation of Y-chromosome specific scaffolds. Table S6. Mapping positions and primers used to generate 9 new B. oleae DNA markers in this study. Table S7. Scaffold/contig localization on B. oleae chromosomes. Table S8. Distribution of the B. oleae Transposable elements in the genome assembly. Table S9. Samples and tissues used for the transcriptome sequencing and assembly. Table S10. Summary of the Trinity transcriptome generated from sequencing all the tissues in Supplementary Table S7. Table S11. Assessment of the completeness of the Trinity de novo transcriptome assembly. Table S12. Orthologous genes among 6 closely related insects. Table S13. Genes that peak at different metamorphic stages. Table S14. Gene ontology enrichment analysis for genes that peak at different metamorphic stages. Table S15. Datasets submitted to NCBI and their corresponding accession numbers and description. Table S16. Sources of proteomes and genomes used in Supplementary figures.

附加文件2：表S1。用于GCA_001188975.2版本基因组组装的测序文库、测序结果及k聚体（k-mer）优化方案。
表S2。3个主流基因组组装结果的质量对比。
表S3。9组不同组装结果的统计信息。
表S4。3个Y染色体组装结果的质量对比。
表S5。用于验证Y染色体特异性支架（scaffold）的引物序列。
表S6。本研究中用于构建9个全新橄榄实蝇（Bactrocera oleae）DNA分子标记的引物及其映射位点。
表S7。橄榄实蝇染色体上的支架（scaffold）/重叠群（contig）定位信息。
表S8。橄榄实蝇基因组组装中转座因子（Transposable element）的分布情况。
表S9。用于转录组测序及组装的样本与组织材料。
表S10。基于补充表S7中所有组织的测序数据构建的Trinity转录组汇总信息。
表S11。Trinity从头（de novo）转录组组装结果的完整性评估。
表S12。6种近缘昆虫间的直系同源基因。
表S13。不同变态发育阶段表达峰值的基因。
表S14。不同变态发育阶段表达峰值基因的基因本体（Gene Ontology, GO）富集分析结果。
表S15。提交至NCBI的数据集及其对应的登录号与说明信息。
表S16。补充图中所使用的蛋白质组与基因组数据的来源。