The first mitochondrial genomes of endosymbiotic rhabdocoels illustrate evolutionary relaxation of atp8 and genome plasticity in flatworms

Abstract

The first three mitochondrial (mt) genomes of endosymbiotic turbellarian flatworms are characterised for the rhabdocoels Graffilla buccinicola, Syndesmis echinorum and S. kurakaikina. Interspecific comparison of the three newly obtained sequences and the only previously characterised rhabdocoel, the free-living species Bothromesostoma personatum, reveals high mt genomic variability, including numerous rearrangements. The first intrageneric comparison within rhabdocoels shows that gene order is not fully conserved even at species levels. Atp8, until recently assumed absent in flatworms, was putatively annotated in two sequences. Selection pressure was tested in a phylogenetic framework and is shown to be significantly relaxed in this and another protein-coding gene: cox1. If present, atp8 appears highly derived in platyhelminths and its functionality needs to be addressed in future research. Our findings for the first time allude to a large degree of undiscovered (mt) genomic plasticity in rhabdocoels. It merits further attention whether this variation is correlated with a symbiotic lifestyle. Our results illustrate that this phenomenon is widespread in flatworms as a whole and not exclusive to the better-studied neodermatans.

Contrasting Host-parasite Population Structure and Role of Host Specificity: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika

“…However, in the case of nad2, an overlap of 1 bp with trnV would allow the presence of the canonical stop codon TAG as was reported in the annotation of C. sclerosus (JQ038226, unpublished). Truncated stop codons have been reported across different lineages of parasitic [68,96,104], endosymbiotic [94] and free living flatworm taxa [105] , and also in early diverging acoelomorphs [106]. An alternative start codon ATT was previously assembled for several flatworm taxa [94,98,107,108] but here it is reported for the first time in dactylogyrid monogeneans, as the start codon of the nad1 gene in C. casuarinus.…”

“…In the present study, the first monogenean and first parasite mitochondrial genome from Lake Tanganyika is presented. A high level of genomic diversity in mitochondria including numerous rearrangements has been previously reported in monogeneans [68], other parasitic or endosymbiotic [94] and free living flatworms [95]. Comparisons at the family level of Dactylogyridae revealed tRNA gene transposition of trnT and between trnL2 and trnR (reviewed in [96]).…”

“…[97] or Syndesmis spp. [94], the lack of rearrangements of the order of PCGs or tRNA genes compared to other species of Cichlidogyrus suggests that gene order is conserved in this monogenean lineage across different clades [70].Similar to its congeners for which the full mitogenome is available, three non-coding regions were assembled in C. casuarinus. Variability in the position, length and GC content in NCRs within and between lineages was previously reported in endosymbiotic/parasitic [68,94] and also free living flatworms [98].…”

“…[94], the lack of rearrangements of the order of PCGs or tRNA genes compared to other species of Cichlidogyrus suggests that gene order is conserved in this monogenean lineage across different clades [70].Similar to its congeners for which the full mitogenome is available, three non-coding regions were assembled in C. casuarinus. Variability in the position, length and GC content in NCRs within and between lineages was previously reported in endosymbiotic/parasitic [68,94] and also free living flatworms [98]. However, the presence of a NCR between the nad5 and cox3 coding genes has been found in all representatives of Dactylogyridae and in other monogenean families such as Diplectanidae [99] and Tetraonchidae [100] for which the mitochondrial genomes are available.…”

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

“…Long stretches of repetitive DNA are notoriously difficult to sequence using conventional Sanger-and second-generation (short-read) sequencing methods [12]. Repetitive elements that extend beyond the usual read length capacity of these platforms (~1 kb for Sanger sequencing; 100-300 bp for second-generation methods) cannot be reliably assembled (e.g., [13]). Although long-range PCR can be used to amplify DNA regions of several kilobases, sequencing through repetitive regions often leads to erroneous and/or ambiguous sequence reads as a consequence of self-priming of randomly-amplified repeat-segments, chimeras and/or jumping PCR artefacts [14,15].…”