Orphan genes, characterized by coding sequences that are entirely unique to a particular species without detectable sequence similarity in the genomes of other organisms are also referred to as "taxonomically restricted genes" or “lineage-specific genes”. The origin of orphan genes involves two main models: Duplication and Divergence model explains the emergence of orphan genes through duplication of gene followed by divergence through neo functionalization, sub functionalization and gene loss / pseudogenization. De Novo model suggest that orphan genes arise from non-coding sequences typically through mutation in regulatory regions of non-coding sequences1.

Various methods, includes BLAST and Phylostratigraphy are employed for the identification of orphan genes. BLAST is a widely used tool for aligning sequences and searching for homologous genes across species. Phylostratigraphy approach helps to differentiate between genes that have a homolog in a closely related species and genes that have evolved independently in the species of interest. Characterization of orphan genes includes introduction of orphan gene into expression vector and transferred into a plant through A. tumefaciens mediated transformation. Transgenic plants were screened for various morphological traits, biotic and abiotic stresses under greenhouse conditions2.

Orphan genes exhibit distinct features such as short open reading frames, few introns and more exons, low GC content in coding sequence, short protein length, high isoelectric point and higher tissue specificity. In the injured or hormone treated tissues, the percent of orphan genes expressed is significantly higher than the nonorphan genes. Hence, orphan genes play a crucial role in responding to environmental stresses.

Notably, QQS (Qua-Quine Starch; At3g30720) is identified as the first plant orphan gene in Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in A. thaliana. QQS transgene is transformed into soybean, rice and maize cultivar through A. tumefaciens mediated transformation and increases the levels of protein and decreases the starch in leaf/seed without affecting the growth and yield of agronomic parameters3. In soybean, AtQQS gene increases the starch and protein in leaf/seed and also encountered resistance to whiteflies and aphids4.

Orphan genes has gradually unveiled the mysterious functions, such as soluble sugar metabolism regulation, male fertility and metagenesis regulation, pollen exine development and regulation of grain shape, grain number, plant height and grain quality appearance in rice.

References

1FAKHAR, A. Z., LIU, J., PAJEROWSKA-MUKHTAR, K. M. AND MUKHTAR, M. S., 2023, The lost and found: unravelling the functions of orphan genes. J. Dev. Biol., 11(2): 27.

2JIANG, M., LI, X., DONG, X., ZU, Y., ZHAN, Z., PIAO, Z. AND LANG, H., 2022, Research advances and prospects of orphan genes in plants. Front. Plant Sci., 13: 947129.

3LI, L., ZHENG, W., ZHU, Y., YE, H., TANG, B., ARENDSEE, Z. W., JONES, D., LI, R., ORTIZ, D., ZHAO, X. AND DU, C., 2019, QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proc. Natl. Acad. Sci., 112(47): 14734-14739.

4TANVIR, R., PING, W., SUN, J., CAIN, M., LI, X. AND LI, L., 2022, AtQQS orphan gene and NtNF-YC4 boost protein accumulation and pest resistance in tobacco (Nicotiana tabacum). Plant Sci., 317: 111198.