BCMA3 Sanger sequencing and structural variant analysis (Brassicaceae)

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Method synopsis

Sanger sequencing of BCMA3 alleles from natural accessions combined with Nanopore long-read genome assembly to identify structural genetic variants affecting glucosinolate biosynthesis.

Synthesized from method descriptions across 2 papers 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 — Ecological factors influence balancing selection on leaf chemical profiles of a wildflower (2021), Nature Ecology & Evolution. Implementations in other papers (listed below) may differ.

1. Perform molecular sequencing of BCMA3
   Sanger sequencing was performed on BCMA3 in a panel of 110 accessions. Long-read genome assembly was conducted using Nanopore sequencing for two parental genotypes (SAD12 and LTM) to identify structural variants around BCMA3.
   Quantities: 110 accessions for Sanger sequencing, 2 genomes for long-read assemblyDuration: Not specifiedConditions: Laboratory sequencing conditions
   Equipment: Sanger sequencing platform, Nanopore sequencing platform

Typical Equipment

• Sanger sequencing platform
• Nanopore sequencing platform

Output Measurements

• BCMA3 sequence variants
• structural variants
• amino acid substitutions

Papers Using This Protocol (2)

Species Studied With This Protocol

Places Where Used