Synteny-based chromosome scaffolding (Pieridae)

Knowledge graph centered on Synteny-based chromosome scaffolding (Pieridae) with 34 nodes and 115 connections. Top connected: Gothic, Pekania pennanti, Colorado East River Valley, Lepidoptera, Mayflies.

Method synopsis

Using synteny analysis with a closely related reference genome to arrange contigs into chromosome-level scaffolds using MUMmer alignment and RagTag scaffolding.

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. Synteny analysis and chromosome assembly
   Used nucmer (MUMmer4, v.4.0.0beta2) to align the PoolSeq-polished P. macdunnoughii genome to the P. napi genome. Used RagTag to group and orient scaffolds against chromosomes 1 through 25 of the P. napi genome, excluding unplaced P. napi scaffolds. Set lower grouping confidence threshold of 80% to avoid chimeric chromosomes. RagTag added 100 N between each joined scaffold, increasing genome length by 5600bp.
   Quantities: 84 contigs aligned to 25 chromosomes, 22 contigs remained unplaced, 5600bp added as gapsDuration: Computational alignment and scaffoldingConditions: Computational analysis
   Equipment: nucmer (MUMmer4, v.4.0.0beta2), RagTag

Typical Equipment

• nucmer (MUMmer4, v.4.0.0beta2)
• RagTag

Output Measurements

• pseudo-chromosomal assembly
• synteny blocks
• chromosome assignments

Papers Using This Protocol (1)

Species Studied With This Protocol

Places Where Used