Genome-Wide Identification, Characterization, and Expression Analysis of Orphan Genes Within Coriander
Orphan genes (<i>OGs</i>) are genes that have no significant sequence similarity with known genes from other species or lineages. Identifying and characterizing <i>OGs</i> have become more feasible with the increasing availability of plant transcriptomes and genome sequences....
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-03-01
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| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/14/5/778 |
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| Summary: | Orphan genes (<i>OGs</i>) are genes that have no significant sequence similarity with known genes from other species or lineages. Identifying and characterizing <i>OGs</i> have become more feasible with the increasing availability of plant transcriptomes and genome sequences. <i>OGs</i> play important roles in response to both biotic and abiotic stresses, contributing to biological functions and lineage-specific traits. This study aimed to identify and characterize <i>OGs</i> in <i>Coriandrum sativum</i> (coriander) using the BLAST method. A total of 941 <i>C. sativum OGs</i> (<i>CsOGs</i>), 1298 Apiaceae-specific genes (<i>ASGs</i>), and 38,508 evolutionarily conserved genes (<i>ECGs</i>) were identified through comparative genomics. Genic feature analyses revealed that <i>CsOGs</i> and <i>ASGs</i>, although part of different gene sets, had shorter gene lengths, a lower proportion of multi-exon genes, and higher GC content than <i>ECGs</i>. <i>OGs</i> were distributed across all 11 chromosomes, with the highest proportion of <i>CsOGs</i> and <i>ASGs</i> found on chromosome A11. RNA-Seq analysis revealed 71 <i>CsOGs</i> uniquely expressed in four different tissues, 61 <i>CsOGs</i> specifically expressed across three growth stages, and five <i>CsOGs</i> with specific expression patterns in different tissues and growth stages. Notably, as determined via qRT-PCR analysis, these five <i>CsOGs</i> presented general or specific expression patterns under normal conditions, but their expression significantly increased after exposure to cold stress, suggesting that they may play a critical role in cold stress response. This study comprehensively identified, characterized, and analyzed the expression of <i>OGs</i> within coriander, which provides a foundation for further research on the functions of coriander <i>OGs</i> in influencing species-specific trait formation and stress response. |
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| ISSN: | 2223-7747 |