An evolutionary preserved intergenic spacer in gadiform mitogenomes generates a long noncoding RNA.

Area of Science:

• Mitochondrial genomics
• Evolutionary biology
• Noncoding RNA research

Background:

• Vertebrate mitogenomes typically lack extensive intergenic sequences.
• The biological roles of intergenic spacers between tRNA(Thr) and tRNA(Pro) genes (T-P spacers) in gadiforms remain largely unknown.

Purpose of the Study:

• To characterize the T-P spacer in European hake (Merluccius merluccius) mitogenomes.
• To investigate the evolutionary presence and function of T-P spacers across diverse gadiform species.
• To elucidate the potential role of T-P spacers in mitochondrial gene expression and regulation.

Main Methods:

• Mitochondome sequencing and characterization.
• Phylogenetic analysis of T-P spacer sequences across 32 gadiform species.
• Intraspecific variation analysis in Atlantic cod (Gadus morhua) using 225 specimens.
• Mito-transcriptome pyrosequencing to identify noncoding RNAs.

Main Results:

• A complex T-P spacer (223-532 bp) was identified in Merluccius merluccius.
• T-P spacers are evolutionarily conserved across 8 families and 28 genera of gadiforms, with complexity correlating with phylogenetic relationships.
• An abundant H-strand specific long noncoding RNA (lncRNA) was detected in Atlantic cod, with the T-P spacer forming its 5' region.

Conclusions:

• The T-P spacer is evolutionarily preserved in gadiform mitogenomes due to a gain of function via a lncRNA.
• The T-P spacer likely enhances the stability of the H-strand specific lncRNA through hairpin structures and protein binding sites.