Additional file 1 of Presence–absence polymorphisms of single-copy genes in the stony coral Acropora digitifera
Creators: name: Takahashi-Kariyazono, Shiho
name: Sakai, Kazuhiko
name: Yohey Terai
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1 Figure S1. Number of PAP genes in 33 A. digitifera individuals. (a) The number of PAP genes (y axis) were plotted against mapping read coverage (x axis) for 33 individuals. (b) The number of PAP genes that were identified as absent homozygous in 1 to 33 individuals. The x-axis represents the numbers of absent homozygous individuals comparing with A. digitifera genome (ver. 1.1) for each PAP gene. The y-axis represents the number of PAP genes. 20% (102) PAP genes appeared in only one individual, and the remaining 80% (n = 414) appeared more than once. Figure S2. Electrophoresis patterns of PAPs among 11 A. digitifera individuals and the structures of PAP loci. The results of PCR products of (a) LOC107329813 and (b) LOC10736915–6. Positions of primers are indicated by arrows, under the schematic representations of genes. Primer names are given under each arrow. M1 and M2 indicate the molecular markers, φX174 HaeIII digest and λ-HindIII digest, respectively. Sample IDs S1601-S1612 are indicated as 01–12. NC indicates negative control. The state of presence (P) and absence (A) estimated by the no coverage region are also shown above the photos. Presence state included both presence homozygous and presence and absence heterozygous samples. In the central panel of (a), one sample (S1603) was expected as presence with a PCR product of present region. However, no PCR product was amplified. (c) The result of PCR for positive control to check the quality of genomic DNA of each sample. (d) Positions of primers for sequence determination of the absent region in LOC107329813. Alignments of 5′ junction sequences and 3′ junction sequences from present and absent alleles are shown in (e) and (f), respectively. (g) Positions of primers for sequence determination of the absent region in LOC10736915–6. (h) Boundaries of absent alleles shown by MinION reads. Figure S3. Combination of presence and absence status of five PAP genes located on one scaffold. Schematic representations of a scaffold (NW_015441940.1) with gene positions (arrows) shown at the top. Rows indicate 33 individuals from two subpopulations. Columns are PAP genes, and the positions are shown by gray arrows at the top. Presence and absence status is shown by white and grey, respectively. Figure S4. The Venn diagram of PAP genes identified in two subpopulations. The numbers of PAP genes specific to subpopulations and shared among subpopulations are in the Venn diagram. Figure S5. Expressions of genes showing PAPs in three individuals. Figure S6. The schematic representation of identification of single-copy genes under functional constraint. Table S1. Overview of high-throughput sequencing. Table S2. Gene IDs and descriptions of PAP genes identified in 33 A. digitifera. Table S3. Percentage of no coverage region and RPKM of 51 PAP genes. Table S4. Description and no coverage (%) of newly-identified single-copy genes. Table S5. Genome or transcriptome data used for blast databases in this study. Table S6. Information for high-throughput sequencing data. Table S7. Primer sequences.