| Summary: | In response to Pi deprivation, <i>phosphate 1</i> (<i>PHO1</i>) is a significant regulator at trans-eQTL hotspots in <i>Brassica rapa</i>. <i>Brassica rapa</i> short-read sequencing data analysis revealed four <i>PHO1</i> paralog genes, <i>PHO1_A</i>, <i>PHO1_B</i>, <i>PHO1_C</i>, and <i>PHO1_D</i>, 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 <i>PHO1</i> 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 <i>PHO1</i> paralogs (ortholog AT1G14040 in <i>Arabidopsis</i>), i.e., <i>PHO1_A</i>, <i>PHO1_B</i>, and <i>PHO1_D</i>, expressed in <i>B. rapa</i> leaf tissues under Pi deficiency. <i>PHO1_A</i>, with transcript ID XM_009150437.2, has five different splice variants found. These splice variants’ truncated proteins demonstrated <i>PHO1_A</i>’s function in P control as opposed to protein encoding.
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