Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints
Research article published in BMC genomics (2018)
Abstract
BACKGROUND: Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. RESULTS: We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. CONCLUSIONS: Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.
Abstract sourced from PubMed (NCBI) for the cited record. See the original publication for the authoritative version.
Резюме
Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications.
Почему это важно для гирудотерапии
This study analyzed codon usage patterns in Hirudinaria manillensis, a blood-sucking leech noted for anticoagulant capacities with potential medical applications, using ~18,000 coding sequences from RNA-Seq data. It found a preference for GC-ending codons, with codon usage shaped primarily by natural selection rather than mutation pressure alone, and that most blood-diet-related genes underwent less adaptive evolution except those with host-homologous sequences. For ASH, the relevance is indirect and foundational: understanding the genetic architecture and evolutionary constraints of a medically relevant leech species could eventually support biotechnological or pharmacological study of its anticoagulant compounds. However, the study reports no identification, isolation, or functional testing of specific anticoagulants, no clinical data, and no direct hirudotherapy findings—it is a molecular evolution and codon-usage analysis.
Цитирование
Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints
Guan DL et al. · BMC genomics, 2018
Связанный клинический контекст
Узнайте, как это исследование связано с клинической практикой
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