A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.

ABSTRACT:

Background

Single nucleotide polymorphisms (SNPs) have emerged as the marker of choice in breeding and genetics, particularly in non-model organisms such as black pepper (Piper nigrum L.), a globally recognized spice crop. This study presents a comprehensive catalog of SNPs in the black pepper genome using data from 30 samples obtained from RNA sequencing and restriction site-associated DNA sequencing, retrieved from the Sequence Read Archive, and their consequences at the sequence level.

Results

Three SNP calling and filtering pipelines, namely BCFtools, Genome Analysis Toolkit (GATK)-soft filtering, and GATK-hard filtering, were employed. Results revealed 498,128, 396,003, and 312,153 SNPs respectively identified by these pipelines, with 260,026 SNPs commonly detected acro

SUBMITTER: Thanthirige HA 

PROVIDER: S-EPMC11912784 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature