Screening of Ty1-<i>copia</i> Retrotransposons in Water Onion (<i>Crinum thaianum</i>), an Endangered Species in Thailand

<i>Crinum thaianum</i>, commonly known as water onion, is an endangered species which is primarily threatened by flood-control-related habitat destruction and illegal harvesting for export, resulting in a sharp population decline; its genetic data still remains poorly studied. Retrotransposon-based markers have received significant attention due to their higher potential informativeness compared to conventional marker methods in genetic diversity studies. This study focused on the screening of Ty1-<i>copia</i> retrotransposons, which have been widely studied and are commonly used as molecular markers in various plant species. Ty1-<i>copia</i> reverse transcriptase (<i>rt</i>) fragments were amplified using degenerate primers targeting conserved regions, followed by cloning and sequencing. Sequences were screened for <i>rt</i> gene homology and translated into amino acid sequences. Lineages were assigned by alignment, and phylogenetic analysis was performed for each isolated sequence with a set of well-classified <i>rt</i> genes. The p-distance values were calculated between the isolated sequences and their closest homologous sequences. A total of 123 isolated sequences were analyzed, representing conserved domains in the <i>rt</i> gene of Ty1-<i>copia</i> elements from <i>C. thaianum</i> and four other <i>Crinum</i> species. The results revealed sequence homology to the Ale, TAR, or Angela lineages, which showed the closest resemblance to 9, 4, and 110 isolated <i>rt</i> sequences, respectively. The conserved <i>rt</i> domain SIYGLKQA was mostly found in Angela (87.27%), while SLY/HGLKQS/L and SLYG/ELKQF/S were mostly found in Ale (66.67%) and TAR (75.00%), respectively. The p-distance values obtained from comparisons with Ty1-<i>copia</i> elements in other plants suggest that the Angela and TAR lineages are more evolutionarily conserved than the Ale lineage. Whilst our study sheds light on the variety of Ty1-<i>copia</i> retrotransposons in <i>C. thaianum</i> and other <i>Crinum</i> species, further research on additional <i>Crinum</i> species and other plants is required to enhance our understanding and facilitate future retrotransposon-based marker development.