Elucidating Quadruplication Event of PHO1 Gene: A Key Regulator of Plant Phosphate Translocation in Brassica rapa

In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in tandem with very high sequence similarity. However,...

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Bibliographic Details
Published in:Horticulturae 2023-07, Vol.9 (7), p.845
Main Authors: Shahbuddin, Dahlia, Rusly, Rosazlina, Shuid, Ahmad Naqib, Ahmad Khair, Ahmad Bukhary
Format: Article
Language:English
Subjects:
Alternative splicing
Artificial chromosomes
Bacterial artificial chromosomes
Bar codes
Brassica
Brassica rapa
Chromosomes
Cloning
Data analysis
Genes
Genetic engineering
genetic regulator
Genetic testing
Genomics
Nucleotide sequence
PHO1
PHO1 gene
phosphate deficiency
Plant tissues
Proteins
Signal transduction
Software
splice variants
Translocation
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Summary:In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in tandem with very high sequence similarity. However, based on short-read genomic sequence data, only three transcripts are accessible. Five bacterial artificial chromosomes (BACs) can be sequenced using a long-read sequencer, which improves de novo assembly and identifies structural variants. The PHO1 gene’s quadruplicating tandem positions in the genomic sequence were confirmed by an analysis of long-read data. Transcript analysis identified only three groups of PHO1 paralogs (ortholog AT1G14040 in Arabidopsis), i.e., PHO1_A, PHO1_B, and PHO1_D, expressed in B. rapa leaf tissues under Pi deficiency. PHO1_A, with transcript ID XM_009150437.2, has five different splice variants found. These splice variants’ truncated proteins demonstrated PHO1_A’s function in P control as opposed to protein encoding.
ISSN:2311-7524
2311-7524
DOI:10.3390/horticulturae9070845