Complete nuclear ribosomal DNA sequence analysis of Pacific abalone Haliotis discus hannai

Mitochondrial DNA Part B

Ding

Han

et al. 2019

Self Cite

The complete mitochondrial genome of Pacific abalone Haliotis discus hannai, an economically valuable shellfish in China, was sequenced and analyzed. The mitogenome was 16,716 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a putative control region. The gene arrangement and orientation were identical with other Haliotis species. Phylogenetic tree was constructed based on 13 PCGs of 7 Haliotidae species to assess their phylogenetic relationship, the tree revealed that H. discus hannai was more closely to H. rufescens and H. iris. ARTICLE HISTORY

supporting

confidence: 79%

mentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Pacific abalone Haliotis discus hannai

Mitochondrial DNA Part B

Ding

Han

et al. 2019

Self Cite

“…The complete rDNA units of R. philippinarum and M. mercenaria were sequenced for the first time in this study. The structural composition and order of the rDNA units were similar to those of other reported eukaryotes [10][11][12]20,21,[23][24][25][26][27][28]. The rDNA unit lengths…”

Section: Discussionsupporting

confidence: 83%

Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria

Wang

Hou

2021

Fishes

Self Cite

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.

“…The rDNA gene orders in these organisms were identical to those in other eukaryotes. Reported rDNA unit lengths vary among taxa, as shown in Table 5, with values of 43 kb (human) (Gonzalez & Sylvester, 1995) and 45 kb (mouse) for mammals (Grozdanov, Georgiev & Karagyozov, 2003); 13.67 kb for fish ( Cyprinus carpio ) (Vera et al, 2003); 12.26 kb ( Brachiola algerae ) (Belkorchia et al, 2008), 9.5 kb ( Plasmodiophora brassicae ) (Niwa et al, 2011) and 8.3 kb ( Eurytrema pancreaticum ) (Su et al, 2018) for parasites; 7.9 kb ( Paracyclopina nana ) (Ki, Park & Lee, 2011), 7.7 kb ( Aurelia sp.1) (Ki, Kim & Lee, 2009) and 9.6–10.7 kb ( Haliotis species) (Guo et al, 2017, 2018; Guo, Hou & Han, 2018) for marine invertebrates; 7.9–8.9 kb ( Oryza sativa ) (Fujisawa et al, 2006) and 8.0–8.9 kb ( Stipa spp.) (Krawczyk et al, 2017) for land plants and 11.76–12.57 kb ( Bangia ) (Xu et al, 2016) and 13.65 kb ( Pyropia yezoensis ) (Li et al, 2016) for sea algae.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the ribosomal DNA repeat unit (rDNA) ofPerna viridis(Linnaeus, 1758) andPerna canaliculus(Gmelin, 1791)

Han

Liang

et al. 2019

PeerJ

Self Cite

Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.