Dataset for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"

Supplementary Tables

Supplementary Table S1: SRA accession list of RNAseq reads.

Supplementary Table S2: Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323.

Supplementary Table S3: Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence.

Supplementary Table S4: Gene expression (log-transformed RPKM) values across the population.

Supplementary Table S5: Locus-specific transcript abundance at individual TE loci (FPKM) across individuals.

Supplementary Table S6: Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population.

Supplementary Table S7: Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci.

Supplementary Table S8: Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome.

Supplementary Table S9: TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).

补充附表

补充表S1：RNA测序读段的SRA（Sequence Read Archive）登录号列表。

补充表S2：参考基因组IPO323中，转座子（Transposable Element, TE）在基因元件以及转录起始位点（Transcription Start Site, TSS）上下游10 kb区间内的基因组定位情况。

补充表S3：病原菌群体中的全基因组转座子插入多态性（TE Insertion Polymorphisms, TIPs），其中0代表转座子缺失，1代表转座子存在。

补充表S4：群体内的基因表达量（以对数转换后的每百万读段每千碱基片段数（Reads Per Kilobase per Million mapped reads, RPKM）表示）。

补充表S5：各样本中单一位点转座子（TE）位点的转录本丰度（以每百万片段每千碱基片段数（Fragments Per Kilobase per Million mapped fragments, FPKM）表示）。

补充表S6：参考基因组IPO323中每个转座子家族的表达拷贝占比，以及群体内每个转座子家族的表达转座子拷贝占比。

补充表S7：基因组中转座子插入多态性（TIPs）与转座子位点上下游600 bp范围内邻近单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的连锁不平衡情况。

补充表S8：病原菌毒力相关性状（PLACP：叶斑分生孢子器覆盖叶面积百分比）与全基因组转座子插入多态性的全基因组关联分析结果。

补充表S9：病原菌群体中与代谢物峰强度变异显著相关的全基因组转座子插入多态性（TIPs，经邦费罗尼校正阈值过滤）。