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linkage map SI.xlsx (12.64 MB)

Supplemental Material for Yin et al., 2020

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posted on 2020-11-02, 15:18 authored by Xiaoshen Yin, Alberto Arias-Pérez, Tevfik Hamdi KitapciTevfik Hamdi Kitapci, Dennis Hedgecock
Table S1 contains a summary of mapping families.
Table S2 contains a list of primers and genotyping-by-sequencing (GBS) common and barcode sequences for ApoI adapters.
Table S3 contains numbers of markers at key steps from genotyping-by-sequencing (GBS) to final linkage maps for six, interrelated F2 families.
Table S4 contains the correspondence between linkage group numbering (Hedgecock et al., 2015) and chromosome numbering of the Chr_v1 chromosome-level C. gigas genome assembly (Qi et al., 2020).
Table S5 contains a compendium constructed with 71,156 SNPs from 19 linkage maps of 12 families.
Table S6 contains a summary of chimeric contigs and chimeric blocks.
Table S7 contains a summary for individual maps input to and consensus map generated from ALLMAPS.
Table S8 contains a summary of comparisons between linkage-based and chromosome-level (Chr_v1) assemblies of sequenced contigs of the Pacific oyster genome.
Table S9 contains the output from the general linear model analysis of recombination rate (RR) data for 12 parents, 10 chromosomes.
Table S10 contains the result of Pearson’s chi-square test for complete spatial randomness of standardized recombination rates in the nominal 10th and 90th percentiles.
Figure S1 contains the length distribution of chimeric blocks on the contig-level assembly of the Chr_v1 genome assembly.


Article title

High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas

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