The complete nuclear ribosomal DNA (nrDNA) cistron sequence of Pyropia yezoensis (Bangiales, Rhodophyta)

Abstract

The complete nuclear ribosomal DNA (nrDNA) cistron sequence of Pyropia yezoensis has been sequenced, of which each unit is composed of the intergenic spacer (IGS), the small-subunit (SSU) ribosomal RNA (rRNA) gene, the internal transcribed spacer 1 (ITS1), the 5.8S rRNA gene, the internal transcribed spacer 2 (ITS2), and the large-subunit (LSU) rRNA gene. This cistron occurs in tandem repeats that can number in 100s to 1000s. Furthermore, in the analysis of the sequence data, we determined that introns were present in the small-subunit rRNA genes, for which the exon sequences (1834 bp) are almost identical. The intron numbers ranging from zero to two in the small-subunit rRNA genes are different between multiple individuals. However, the full length of the large-subunit rRNA genes is 4770 bp without any introns, and the 5.8S rRNA gene is 159 bp. Moreover, the 5′ and 3′ terminal sequences of the genic regions of the ribosomal cistron are extremely conservative even among various species in red alga. In addition, the range for ITS1 is 371-372 bp and for ITS2 is 532 to 535 bp. The IGS is 5984 bp in length and possesses upstream direct repeats, downstream repeats, and middle inverted repeats that make sequencing untoward. This is the first time that the complete nucleotide of the IGS region of P. yezoensis has been sequenced. The provision of the full length of nrDNA cistron will offer useful information to be widely utilized for identification, taxonomic relationships, and phylogenies in red algae.

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

“…While the 18S and 26S subunits are frequently employed in deep-level (e.g., suprafamilial) phylogenetic reconstructions (Nickrent and Soltis 1995;Soltis et al 1997a, b;Ashworth 2000;Soltis et al 2000;Fan and Xiang 2003), the ITS1, 5.8 S and ITS2 regions are often used for estimating shallow level (e.g., infrafamilial) relationships (Baldwin et al 1995;Álvarez and Wendel 2003;Mort et al 2007;Calonje et al 2009;Smith et al 2011;Song et al 2017). Notably, the entire nrDNA cistron has been scarcely used in plant phylogenetics; to our knowledge it has only been studied in red algae (Li et al 2016;Xu et al 2016;He et al 2017). As shown in our phylogenetic results for the five S. subg.…”

Health Functionality and Quality Control of Laver (Porphyra, Pyropia): Current Issues and Future Perspectives as an Edible Seaweed

“…The plastid and mitochondrial genomes of red algae were first analyzed in Porphyra purpurea (Roth) C. Agardh, 1824 [144][145][146], with subsequent genomic research conducted using next-generation sequencing technologies [146][147][148][149][150][151][152][153][154]. Laver is regarded as the model genome for red algae, and detailed analysis has provided data for phylogenetic, taxonomic, and evolutionary studies [146,147,155].…”

“…Whole genome sequencing and genomic feature P. umbilicalis -Genome governing nutritional/functional values linked to the growth and survival strategy of laver under stressful condition of natural habitat (intertidal zone) [147] P. yezoensis -First report on the genome sequence of nuclear ribosomal DNA (nrDNA) cistron [149] P. yezoensis -Genome sequence and annotated functional genes from P. yezoensis -Identification of photosynthesis system and key genes governing color of laver [154] Genome-wide identification of functional genes P. yezoensis -Gene structure associated with mitogen-activated protein kinases from P. yezoensis (PyMAPKs) […”

Peer Review #2 of "Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791) (v0.1)"

“…Reported rDNA unit lengths vary among taxa, as shown in Table 5, with values of 43 kb (human) (Gonzalez and Sylvester, 1995) and 45 kb (mouse) for mammals (Grozdanov et al, 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 et al, 2011), 7.7 kb (Aurelia sp.1) (Ki et al, 2009) and 9.6-10.7 kb (Haliotis species) (Guo et al, 2017, 2018 a b) 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. Meanwhile, the rDNA lengths of P. viridis and P. canaliculus were 8.6 and 7.6 kb, respectively.…”

“…The coding regions are highly conserved between organisms, and have been selected as genetic markers for higher-level relationships within the molluscan (Distel, 2000;Passamaneck et al, 2004;Combosch and Giribet, 2016). Whereas non-transcribed regions (ITS1, ITS2 and IGS) exhibit high structural variability (Li et al, 2016;Huang et al, 2017;. The IGS region often contains repeat fragments, promoter and enhancer sites.…”