NLR DNA copy-number expansion outpaces accumulation of predicted coding-intact copies
Abstract
Whether nucleotide-binding leucine-rich repeat (NLR) DNA copies and predicted coding-intact copies accumulate proportionally within homologous neighbourhoods remains unresolved. We compared these counts across 173 anchor-defined neighbourhoods in 11 Capsicum genomes. After accounting for neighbourhood and genome effects, predicted coding-intact copies increased less than proportionally with DNA copies. DNA-copy doubling corresponded to 1.48-fold and 1.84-fold increases in expected coding counts under strict and inclusive definitions, respectively. The strict association persisted across sequence and sampling controls, with highly expanded arrays and heterogeneous coding recovery affecting interpretation. An independently defined panel of 17 Arabidopsis thaliana accessions reproduced sublinear scaling using curated gene counts. Matched pepper RNA-seq showed a transcript-support gradient across predicted coding states. At DH06, a near-megabase segmental duplication in C. pubescens contained intact and disrupted family pairs. Copy-specific HiFi reads placed the same F396 coding lesions in both physical blocks. Together, these results reveal a recurrent relationship between NLR array size and coding composition in the surveyed plant systems. Interpreting DNA expansion together with coding state provides a more informative basis for comparing NLR repertoires and prioritizing immune-gene candidates.
Read the paper
Related studies
- Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts
- For a Healthy Histone Code, a Little SUMO in the Tail Keeps the Acetyl Away
- Discovering a binary CTCF code with a little help from BORIS
- Article Commentary: Stabilizing the Code–-Methods to Preserve RNA Prove Their Worth
- Foreword to the Special Issue for the RINTC (The Implicit Seismic Risk of Code-Conforming Structures) Project
- Commentary: Promoting Health and Well-being in Pediatric Primary Care Settings: Using Health and Behavior Codes at Routine Well-child Visits
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.