Genetic mapping files

High-throughput genetic mapping (Folder “Genetic mapping files”) The datasets in items 1 to 3 relate to high-throughput genotyping, supplemented with microsatellite genotyping to ascertain parentage of progeny with more than a single sire and/or dam, and to map the microsatellite markers. Initial bioinformatic processing is described in the “Data_description” file provided, and was followed by formatting for genetic mapping analysis using LepMap3 software (Rastas 2017). Rastas, P., 2017 Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33: 3726-3732. doi: 10.1093/bioinformatics/btx494 https://sourceforge.net/p/lep-map3/wiki/LM3 Home/ Most files are Excel files of genotypes and allele counts, or genotypes in the format required by LepMap3, or text files. 1. Microsatellite sequences found in the guppy female and male genome assemblies using the PERF software v0.4.5 (Avvaru et al., 2018). Excel files: Guppy_genes_and_microsats_on_femaleLG12_malechr12_KK07July2021 Guppy_genes_and_microsats_on_unplaced_scaffolds_updated3rdNov2020 Avvaru, A. K., D. Sowpati and R. Mishra, 2018 PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences Bioinformatics 34: 943–948. doi: 10.1093/bioinformatics/btx721 2. Excel file with information about genes on the guppy sex chromosome in the male and female assemblies, and on the homologous chromosome (Xm8) in the platyfish, Xiphophorus maculatus: “Guppy_female_Gene_positions_on_Guppy_male_and_Platyfish” 3. Genetic map input and results files a. Folder “Files for all individual families” contains sparse maps, estimated mostly with microsatellite markers (including some families not analysed in detail, and therefore not listed in Supplementary Table 1 of the associated manuscript: AHPGrp3) b. ALP2_B2_LAH_QLP1_BI_QHPGrp5_mappings_2021: microsatellite marker genotypes, showing assignments of parentage for individual progeny in the ALP2B2 family. HIGH-THROUGHPUT GENOTYPING EXPERIMENTS (3 folders): The list below shows the contents of the folders for each experiment. c. EXPERIMENT 2 (NGS1242. LAH, QHPG5 and ALP2B2 families, plus guppy natural population samples) i. NGS_1242_DNA-samples_for.review.Deborah.190212 ii. SNPs targeted: File “probeStats_high-specificity_ST5041G_1_1781.xlsx” iii. hiseq_platelayouts_Dec2018 iv. Genotypes_targeted_Bowtie2-Genome_Freebayes-ploidy2-min-count-8_NGS1242_2019-05-20 (genotyping results with allele counts) d. EXPERIMENT 3 (NGS2589. QHPG5 family plus Micropoecilia picta, parae and bifurca) i. NGS2589_sample_form_sn_211222 ii. probe_ST5271G_1_3272_10k-selection iii. LGCG plates layout 1.2 Experiment 3 iv. Variants_all_GMCF8_QHPG5_NGS2589_2022-02-21 (genotypes, allele counts) v. Variants_all_GMCF8_picta_NGS2589_2022-02-21 (genotypes, allele counts) vi. Variants_all_GMCF8_parae_NGS2589_2022-02-21 (genotypes, allele counts) vii. Variants_all_GMCF8_bifurca_NGS2589_2022-02-21 (genotypes, allele counts) viii. “EX3_LG12_SNPs_coded_for_LepMap3.txt”: QHPG5 family genotypes for mapping e. EXPERIMENT 4 (NGS2945. QLP1B1 family plus Micropoecilia species as in Experiment 3, but with smaller sample sizes) i. LG12 and LG16 targets: file “probeStats_ST5271G_3_3633” ii. Names of samples and positions in the plates: File ‘NGS2589_sample_form v2’ iii. July 2022 plate layout for experiment 4-1 iv. Data_description.pdf: file with description of bioinformatic analysis by LGCG v. Genotypes_targeted_Bowtie2-Genome_all-min-count-8_NGS2945_2022-10-22 (Excel file with genotypes, allele counts) vi. LG16 for LepMap3: File “EX4_QLP1B_LG16_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx” vii. LG12 for LepMap3: File “EX4_QLP1B_LG12_tabbed_for_LepMap3.txt”, and “EX4_QLP1B_LG12_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx”

高通量遗传作图（文件夹"遗传作图文件"）
第1至3项数据集涉及高通量基因分型，辅以微卫星基因分型以确定存在多个父本和/或母本的子代的亲权，并对微卫星标记进行遗传作图。初始生物信息学处理流程见所附"Data_description"文件，随后使用LepMap3软件（Rastas, 2017）完成遗传作图分析的格式转换。相关文献引用：Rastas, P., 2017 Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. 《生物信息学》33: 3726-3732. doi: 10.1093/bioinformatics/btx494 https://sourceforge.net/p/lep-map3/wiki/LM3 Home/
本数据集大部分文件为包含基因型与等位基因计数的Excel文件、符合LepMap3要求格式的基因型文件，或纯文本文件。

1. 使用PERF软件v0.4.5（Avvaru等, 2018）在孔雀鱼（guppy）雌性与雄性基因组组装版本中鉴定得到的微卫星序列。相关Excel文件如下：
Guppy_genes_and_microsats_on_femaleLG12_malechr12_KK07July2021
Guppy_genes_and_microsats_on_unplaced_scaffolds_updated3rdNov2020
相关文献引用：Avvaru, A. K., D. Sowpati and R. Mishra, 2018 PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences 《生物信息学》34: 943–948. doi: 10.1093/bioinformatics/btx721

2. 包含孔雀鱼（guppy）性染色体（雌性与雄性组装版本）以及花斑剑尾鱼（Xiphophorus maculatus）同源染色体（Xm8）上基因信息的Excel文件："Guppy_female_Gene_positions_on_Guppy_male_and_Platyfish"

3. 遗传作图输入文件与结果文件

a. 文件夹"所有家系作图文件"包含稀疏遗传图谱，多数通过微卫星标记估算得到（包含部分未进行详细分析、因此未在相关论文补充表1中列出的家系：AHPGrp3）
b. ALP2_B2_LAH_QLP1_BI_QHPGrp5_mappings_2021：微卫星标记基因型文件，展示了ALP2B2家系中各子代的亲权分配情况。

高通量基因分型实验（共3个文件夹）
下文列出各实验文件夹的具体内容：

c. 实验2（NGS1242：涉及LAH、QHPG5与ALP2B2家系，以及孔雀鱼自然种群样本）
i. NGS_1242_DNA-samples_for.review.Deborah.190212
ii. 靶向单核苷酸多态性位点（SNPs）文件："probeStats_high-specificity_ST5041G_1_1781.xlsx"
iii. hiseq_platelayouts_Dec2018
iv. Genotypes_targeted_Bowtie2-Genome_Freebayes-ploidy2-min-count-8_NGS1242_2019-05-20（包含基因型与等位基因计数的基因分型结果文件）

d. 实验3（NGS2589：涉及QHPG5家系以及小花鳉属（Micropoecilia）picta、parae与bifurca物种）
i. NGS2589_sample_form_sn_211222
ii. probe_ST5271G_1_3272_10k-selection
iii. LGCG板布局1.2 实验3
iv. Variants_all_GMCF8_QHPG5_NGS2589_2022-02-21（包含基因型与等位基因计数的变异位点文件）
v. Variants_all_GMCF8_picta_NGS2589_2022-02-21（对应picta样本的变异位点基因型与等位基因计数文件）
vi. Variants_all_GMCF8_parae_NGS2589_2022-02-21（对应parae样本的变异位点基因型与等位基因计数文件）
vii. Variants_all_GMCF8_bifurca_NGS2589_2022-02-21（对应bifurca样本的变异位点基因型与等位基因计数文件）
viii. "EX3_LG12_SNPs_coded_for_LepMap3.txt"：用于遗传作图的QHPG5家系基因型文件

e. 实验4（NGS2945：涉及QLP1B1家系，以及与实验3相同的小花鳉属物种，但样本量更小）
i. LG12与LG16靶向位点文件："probeStats_ST5271G_3_3633"
ii. 样本名称与板内位置文件："NGS2589_sample_form v2"
iii. 2022年7月实验4-1板布局
iv. Data_description.pdf：LGCG撰写的生物信息学分析说明文件
v. Genotypes_targeted_Bowtie2-Genome_all-min-count-8_NGS2945_2022-10-22（包含基因型与等位基因计数的Excel格式基因型文件）
vi. 用于LepMap3分析的LG16文件："EX4_QLP1B_LG16_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx"
vii. 用于LepMap3分析的LG12文件："EX4_QLP1B_LG12_tabbed_for_LepMap3.txt"与"EX4_QLP1B_LG12_SIBSHIPs3,5,2_tabbed_for_LepMap3.xlsx"