Abstract
Ruditapes philippinarum and Mercenaria mercenaria are economically important bivalve species. The complete ribosomal DNA (rDNA) unit sequences of R. philippinarum and M. mercenaria, with as-sembled rDNA unit lengths of 12,910 and 12,100 bp, respectively, were obtained in this study for the first time. The rDNA unit structural organisation was similar to that in other eukaryotes, in-cluding the following elements in order: 18S rRNA-internal transcribed spacer 1 (ITS1); 5.8S rRNA-ITS2-28S rRNA-intergenic spacer (IGS) (3′ external transcribed spacer (ETS); non-transcribed spacer (NTS)-5′ ETS). The genetic differences between R. philippinarum and M. mercenaria were mainly attributable to non-coding regions (ITS1, ITS2 and IGS), especially the IGS region. The boundaries of putative 3′ ETS, NTS and 5′ ETS were confirmed. Seven and three sub-repeat fragments were found in R. philippinarum and M. mercenaria, respectively. These frag-ments ranged from 4 to 154 bp in length, and were located at the NTS and 5′ ETS regions. Five and six cytosine–guanine (CpG) islands were detected in R. philippinarum and M. mercenaria, respec-tively, and these covered 85.58% and 79.29% of the entire IGS sequence, respectively. The phylo-genetic tree was constructed based on Veneridae ITS and 18S rRNA sequences using the maxi-mum likelihood (ML) method. The ML tree based on ITS revealed that species within the same genus clearly clustered together with relatively high supporting values, and all the genera were recovered as monophyletic. The phylogenetic analyses using 18S rRNA provided a weaker phy-logenetic signal than ITS.
Highlights
Published: 17 September 2021Veneridae is one of the most diverse families of molluscs, with approximately800 species [1,2]
The complete ribosomal DNA (rDNA) units of R. philippinarum and M. mercenaria were determined after amplification, sequencing and assembly
We analysed the main features of intergenic spacer (IGS) functional elements, namely, the TIS, TTS and SR and CpG islands
Summary
Published: 17 September 2021Veneridae is one of the most diverse families of molluscs, with approximately800 species [1,2]. Many Veneridae species are economically important due to their huge abundance in benthic environments, such as the Manila clam. The classification system and phylogenetic re-lationships of Veneridae have been based mainly on morphological characteristics and molecular data (mitochondrial and nuclear sequences) [1,2,4,5,6], which are currently un-der debate. Problems with existing classification methods are attributed to (1) the con-vergence of the evolutionary and phenotypic plasticity of morphological traits in most venerids [6]; (2) double uniparental inheritance (DUI) of mitochondrial DNA in some Veneridae species [7,8,9];. Nuclear ribosomal DNA (nrDNA) is usually organised in long tan-dem repeats that form nucleolar organising regions in chromosomes [10,11].
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