PoolSeq nucleotide diversity analysis (Pieridae)

Knowledge graph centered on PoolSeq nucleotide diversity analysis (Pieridae) with 31 nodes and 109 connections. Top connected: Ligusticum porteri, Lepidoptera, Papilio, non-native plants, Pieris napi.

Method synopsis

Population genetic analysis using pooled sequencing data to estimate nucleotide diversity across chromosomes and validate sex chromosome identity through coverage analysis.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — The genome of the Margined White butterfly (Pieris macdunnoughii): sex chromosome insights and the power of polishing with PoolSeq data (2021), Genome Biology and Evolution. Implementations in other papers (listed below) may differ.

1. Population genetic analysis
   Mapped PoolSeq reads to final pseudo-chromosomal assembly with NextGenMap and filtered for proper pairs. Generated pileup file and used PoPoolation (v.1.2.2) to filter insertions and deletions before calculating nucleotide diversity (π) over 50,000bp windows in each pseudo-chromosomal contig.
   Quantities: 50,000bp sliding windows, 4,876,412 variable sites identified, genome-wide mean autosomal π of 0.0060Duration: Computational analysisConditions: Computational analysis
   Equipment: NextGenMap, Samtools v.1.0, PoPoolation (v.1.2.2)

Typical Equipment

• NextGenMap
• Samtools v.1.0
• PoPoolation (v.1.2.2)

Output Measurements

• nucleotide diversity
• coverage ratios
• variable site counts

Papers Using This Protocol (1)

Species Studied With This Protocol