Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera (Rhodophyta)

Hwang, Mi Sook; Kim, Seung-Oh; Ha, Dong-Soo; Lee, Jee Eun; Lee, Sang-Rae

doi:10.1007/s11816-013-0281-4

Cited by 19 publications

(26 citation statements)

References 26 publications

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“…Variation in the size of P. yezoensis mtDNA was largely due to the different number of mitochondrial group II introns in the rnl and cox1 genes. The differing number of introns was previously reported on in red algae mtDNA at the interspecific level (Hwang et al, 2013;Xu et al, 2018a). In this study, we detected intraspecific variation in intron structure across the 53 Chinese P. yezoensis strains.…”

Section: Polymorphisms At the Intraspecific And Intraindividual Levelssupporting

confidence: 62%

“…The observed differences were mainly caused by different numbers of mitochondrial group II introns in the large subunit ribosomal RNA (rnl) gene and the cytochrome c oxidase subunit 1 (cox1) gene. Recent studies have shown that in the Pyropia species, the rnl gene is composed of four coding regions and the cox1 gene is composed of five coding regions (Hwang et al, 2013). According to the presence of the intron, the 53 individuals displayed five structural patterns of the rnl gene and three of the cox1 gene (Figure 3).…”

Section: Structural Variation Of P Yezoensis Organellar Genomesmentioning

confidence: 99%

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Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Tang

et al. 2019

Front. Mar. Sci.

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Pyropia yezoensis is an economically important marine algae crop that, due to its large economic value, has generated considerable interest in the development of breeding programs to improve its production rates. Here, we sequenced the complete mitochondrial and plastid genomes of the P. yezoensis strain RZ-58 using the PacBio RS II sequencing technology. The mitochondrial genome (mtDNA) is 41,692 bp in size with an overall guanine-cytosine (GC) content of 32.72%, and the plastid genome (ptDNA) is 191,977 bp with a GC content of 33.09%. The complete mitochondrial and plastid genomes of 53 individuals from three geographical populations were then resequenced using the next-generation sequencing (NGS) technology to characterize their molecular features. When compared, the plastid genomes displayed similar genomic lengths and conserved gene synteny. However, mitochondrial genomes were quite different in length, which was mainly due to the different patterns of intron distributions. Single-nucleotide polymorphisms (SNPs) were examined to evaluate the genetic diversity of different geographical populations. High diversity was observed across the whole collection with moderate genetic variation between populations. In total, there were 463 and 366 highquality SNPs detected in the mtDNA and ptDNA, respectively. The Qingdao wild group has the highest diversity with a mean pi of 0.00348 for mtDNA and 0.000388 for ptDNA, while the Yantai group had the lowest diversity. Cluster-based grouping and principal component analysis revealed three subpopulations in the whole collections. However, a genetic break of organellar DNA was observed in populations at sympatric localities, which was inferred as the result of historic biogeographic events. Our findings provide important information to guide marker-assisted selective breeding of Chinese P. yezoensis in the future.

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Section: Polymorphisms At the Intraspecific And Intraindividual Levelssupporting

confidence: 62%

Section: Structural Variation Of P Yezoensis Organellar Genomesmentioning

confidence: 99%

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Tang

et al. 2019

Front. Mar. Sci.

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“…2). LCB analysis and linearized barcode alignments of the 15 Pyropia generated here, against those of published Pyropia and Porphyra 2123242526, identified 18 conserved gene regions (Fig. 4).…”

Section: Resultsmentioning

confidence: 94%

Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

Hughey

Gabrielson

Rohmer

et al. 2014

Sci Rep

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Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm2 of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

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“…Examination of these two species in the field where they co-occur in Pacific Grove, found that the margins of freshly collected P. lanceolata are more strongly ruffled than P. nitida. The mitogenome of P. nitida is intermediate in length 35 313 bp (29 156 bp -Wildemania schizophylla to 42 268 bp -Pyropia tenera) and consistent in gene number with 53 genes (49 genes -P. perforata to 57 genes -P. yezoensis) to other published mitochondrial genomes for the family (Burger et al, 1999;Hwang et al, 2013;Kong et al, 2013;Mao et al, 2012;Reith & Munholland, 1995;Smith et al, 2012;Wang et al, 2013). Like P. nitida, five species in the Bangiaceae contain orf550, and four species orf831.…”

Section: Discussionmentioning

confidence: 71%

Identification of a new marine algal species Pyropia nitida sp. nov. (Bangiales: Rhodophyta) from Monterey, California

Harden

Morales

Hughey

2015

Mitochondrial DNA Part A

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An unidentified marine red algal species classified in Pyropia J. Agardh was discovered from Monterey, CA. Morphological, barcode, and complete mitochondrial genome analysis of the alga support its recognition as a new species, Pyropia nitida sp. nov. The species is a high-intertidal, winter annual that is lanceolate in shape, monostromatic, and dioecious. Based on CO1 sequences, P. nitida is closely allied with the P. nereocystis clade. The mitogenome of P. nitida is 35 313 bp in length and contains 53 genes, including two ribosomal RNAs, 24 transfer RNAs, four ribosomal proteins, two ymfs, four ORFs, and 17 genes involved in electron transport and oxidative phosphorylation. The results support the recognition of P. nitida as distinct from the morphologically similar P. lanceolata.

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Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera (Rhodophyta)

Cited by 19 publications

References 26 publications

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

Identification of a new marine algal species Pyropia nitida sp. nov. (Bangiales: Rhodophyta) from Monterey, California

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