A panel of 66 peanut lines that encompass foundational historic lines and lines that represent the phenotypic diversity of the NCSU Virginia-type peanut breeding program, were selected for whole genome sequencing (WGS) to assess the genetic variability present in the breeding program. The panel was composed of 11 historical Virginia-type peanut lines, 14 modern Virginia-type peanut lines, 35 germplasm lines (generally unimproved plant introductions or landraces) - most of which are heavily incorporated into the NCSU breeding population, 2 parental lines, and 4 Runner-type peanut lines (Table S1
Truseq nano dna prep kit
Manufactured by Illumina
Sourced in United States
The TruSeq Nano DNA Library Prep Kit is a library preparation kit designed for Illumina sequencing platforms. It is used to generate DNA libraries from a wide range of input DNA amounts, from 100 ng to 1 μg. The kit utilizes a tagmentation-based approach for library construction, which involves enzymatic fragmentation and adapter ligation in a single step. The resulting libraries are then amplified and purified for Illumina sequencing.
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Lab products found in correlation
Novaseq 6000 platform, by Illumina (1 mentions)
Dneasy plant mini kit, by Qiagen (1 mentions)
Novaseq 6000 sequencing system, by Illumina (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Novaseq 6000, by Illumina (1 mentions)
Bigdye v3, by Thermo Fisher Scientific (1 mentions)
3500xl genetic analyzer, by Thermo Fisher Scientific (1 mentions)
Nextseq 500, by Illumina (1 mentions)
5 protocols using truseq nano dna prep kit
1
Whole Genome Sequencing of Diverse Peanut Germplasm
2
DNA Library Construction from EMS Mutants
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The DNA library construction from EMS mutants was prepared using Truseq Nano DNA Prep Kit (Illumina, San Diego, CA, USA). The quality was verified by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA), then the passed libraries were loaded onto NovaSeq 6000 Sequencing system (Illumina, San Diego, CA, USA) by DNALink, South Korea (https://www.dnalink.com ), as instructed in the manufacturer’s protocols. The reads were quality checked and filtered by fastp(Chen et al., 2018 (link)). The clean reads were aligned to the reference genome of TAIR10 and genetic variants were called according to SIMPLE pipeline (Wachsman et al., 2017 (link)).
3
Assembly of E. keratini EPI-7T Genome
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E. keratini EPI-7T genomic DNA was sequenced at the Teragen Bio (Theragen Bio, Seongnam, Republic of Korea) by Illumina NovaSeq 6000 (Illumina Inc., San Diego, CA, USA). Illumina PE libraries were prepared using the TruSeq Nano DNA Prep kit (Illumina, San Diego, CA, USA) in terms of the included instructions. Subsequently, we prepared the PacBio SMRTbell raw sequence data downloaded from COSMAX R&I Center, Seongnam, Republic of Korea.
With the Illumina PE libraries and PacBio SMRTbell raw sequence data, the E. keratini EPI-7T genome was assembled with the de novo hybrid strategy. First, the Canu v1.7 generated long-read assembly contigs from PacBio SMRTbell raw sequence data with default option [23 (link)]. Next, to correct and improve accuracy, Illumina PE reads were integrated onto the draft genome using BWA mem v.0.7.17 (Wellcome Trust Sanger Institute, Cambridge, UK) [24 ]. Then, a polishing round was performed five times using pilon v.1.22 (Broad Institute of MIT and Harvard, Cambridge, MA, USA) [25 (link)].
With the Illumina PE libraries and PacBio SMRTbell raw sequence data, the E. keratini EPI-7T genome was assembled with the de novo hybrid strategy. First, the Canu v1.7 generated long-read assembly contigs from PacBio SMRTbell raw sequence data with default option [23 (link)]. Next, to correct and improve accuracy, Illumina PE reads were integrated onto the draft genome using BWA mem v.0.7.17 (Wellcome Trust Sanger Institute, Cambridge, UK) [24 ]. Then, a polishing round was performed five times using pilon v.1.22 (Broad Institute of MIT and Harvard, Cambridge, MA, USA) [25 (link)].
4
Targeted Resequencing of Kooiker Dogs
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One affected Kooiker dog and two unaffected control dogs were selected for targeted resequencing of genomic DNA. After DNA was sheared, fragments of all exons and adjacent intronic 35 bp of genes from the critical region were enriched for and amplified using an Agilent SureSelect in-solution enrichment design. Library preparation was performed using the Illumina TruSeq® Nano DNA Prep Kit. The enriched libraries were sequenced on an Illumina MiSeq. Mapping and variant calling of the paired-end reads of 150 bases were achieved using a custom bioinformatic pipeline based on the Burrows–Wheeler Aligner algorithm (Li and Durbin, 2009 (link)). The SAMtools was used for annotation and initial variant calling against the reference genome CanFam3.1 (Li et al., 2009 (link)). The variants were curated by comparing the allele frequencies of detected variants in a cohort of 590 dogs (Supplementary Table S2 ). Two variants of interest were further analyzed in all available dogs of the HNM pedigrees by chain termination sequencing using the BigDye v3.1 (Applied Biosystems) on a Genetic Analyzer 3500xL (Applied Biosystems). The oligonucleotides used for PCR amplification and sequencing reactions are specified in Supplementary Table S1 .
5
Comparative Genomics of Fragaria Species
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Whole-genome shotgun resequencing analysis was performed across the 14 diploid Fragaria species. PE libraries with an insert size of 500 bp were constructed with the TruSeq Nano DNA Prep Kit (Illumina) and sequenced on NextSeq 500 (Illumina) in paired-end, 151-bp mode. The obtained sequences were mapped onto the pseudomolecule sequences (FAN_r2.3.pseudomolecule) by Bowtie 2 [20] , and SNPs were called the same as in the above ddRAD-Seq analysis. The called candidate SNPs were filtered out according to the following criteria: include only genotypes supported by reads ≥ 10 (--minDP 10); include only sites with quality values ≥ 999 (--minQ 999); exclude sites with ≥ 50% missing data (--max-missing 0.5); include only sites with minor allele frequencies ≥ 0.2 (--maf 0.2). Dendrograms of the 14 diploid species and F. × ananassa were drawn with TASSEL 5 [18, (link)32] (link).
Comparative analyses of the genome sequences between the two phased sequences of the FAN_r2.3.pseudomolecule and between the two species, F. × ananassa (FAN_r2.3.pseudomolecule) and F. vesca (v1.1), were performed with NUCmer of the MUMmer package [23] . Comparisons between the FAN_r2.3.pseudomolecule and the Camerosa genome[13] were performed by using D-Genesis [33] (link).
Comparative analyses of the genome sequences between the two phased sequences of the FAN_r2.3.pseudomolecule and between the two species, F. × ananassa (FAN_r2.3.pseudomolecule) and F. vesca (v1.1), were performed with NUCmer of the MUMmer package [23] . Comparisons between the FAN_r2.3.pseudomolecule and the Camerosa genome[13] were performed by using D-Genesis [33] (link).
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