Mitochondrial and chloroplast genome sequences of Ulva ohnoi, a green-tide-forming macroalga in the Southern coastal regions of Japan

Suzuki, Shigekatsu; Yamaguchi, Haruyo; Hiraoka, Masanori; Kawachi, Masanobu

doi:10.1080/23802359.2018.1483778

Cited by 20 publications

(14 citation statements)

References 26 publications

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“…Horizontal bars represented the size of the Ulva cpDNAs. Cai et al, 2017;Wang et al, 2017;Suzuki et al, 2018;Jiang et al, 2019;Fort et al, 2020). The variation in genome size of U. compressa cpDNAs at intraspecific level was mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of noncoding intergenic spacer regions (Figure 1), which was similar to that observed in Ulva mitochondrial genomes (Liu F. et al, 2020).…”

Section: Features and Architecture Of U Compressa Chloroplast Genomessupporting

confidence: 56%

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Liu

Melton

2021

Front. Mar. Sci.

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To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

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Section: Features and Architecture Of U Compressa Chloroplast Genomessupporting

confidence: 56%

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Liu

Melton

2021

Front. Mar. Sci.

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“…This genome is a circular DNA molecule consisting of 102,899 bp (Fig. 1), which is similar to the reported sizes for U. ohnoi (103,313 bp), U. flexuosa (89,414 bp), U. lactuca (96,005 bp) and other Ulva species (Cai et al, 2017;Wang et al, 2017;Suzuki et al, 2018).…”

Section: Resultssupporting

confidence: 83%

Construction of genomic marker sets based on the chloroplast genome of a green alga, Ulva pertusa (syn. Ulva australis), leads to simple detection of Ulva species

2020

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In closed sea areas such as Tokyo Bay, a phenomenon known as a green tide often occurs, in which large amounts of Ulva seaweed grow abnormally and form mats along the coast. This is currently a serious environmental problem. Green tides are generated by the explosive growth of multiple types of Ulva algae. However, many Ulva species show similar characteristics to each other and are indistinguishable by appearance, making it difficult to identify the Ulva algae in green tides. In this study, we determined the entire nucleotide sequence of the chloroplast genome of Ulva pertusa (syn. Ulva australis) and identified two large inversions of gene order, suggesting the occurrence of genome inversions. We also detected structural polymorphisms among Ulva chloroplast genomes. Ulva pertusa was classified in a different clade from that containing U. lactuca and U. ohnoi, suggesting that U. pertusa is evolutionarily divergent from these species. Based on this knowledge, we constructed a genetic diagnosis system for Ulva algae. Using this approach, we established a simple method that can determine the species of Ulva algae by PCR using specific molecular markers, through which representative Ulva species such as U. lactuca, U. ohnoi and U. pertusa were easily distinguished.

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“…2017; U. fasciata, Melton and Lopez‐Bautista 2017; U. ohnoi, Suzuki et al. 2018; U. mutabilis , NCBI reference sequence NC_043860; U. prolifera, NCBI reference sequence NC_036137; U. linza, Wang et al. 2017; and U. lactuca, Hughey et al.…”

Section: Discussionmentioning

confidence: 99%

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild

Fort

McHale

Cascella

et al. 2020

Journal of Phycology

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Foliose Ulva spp. have become increasingly important worldwide for their environmental and financial impacts. A large number of such Ulva species have rapid reproduction and proliferation habits, which explains why they are responsible for Ulva blooms, known as “green tides”, having dramatic negative effects on coastal ecosystems, but also making them attractive for aquaculture applications. Despite the increasing interest in the genus Ulva, particularly on the larger foliose species for aquaculture, their inter‐ and intra‐specific genetic diversity is still poorly described. We compared the cytoplasmic genome (chloroplast and mitochondrion) of 110 strains of large distromatic foliose Ulva from Ireland, Brittany (France), the Netherlands and Portugal. We found six different species, with high levels of inter‐specific genetic diversity, despite highly similar or overlapping morphologies. Genetic variation was as high as 82 SNPs/kb between Ulva pseudorotundata and U. laetevirens, indicating considerable genetic diversity. On the other hand, intra‐specific genetic diversity was relatively low, with only 36 variant sites (0.03 SNPs/kb) in the mitochondrial genome of the 29 Ulva rigida individuals found in this study, despite different geographical origins. The use of next‐generation sequencing allowed for the detection of a single inter‐species hybrid between two genetically closely related species, U. laetevirens, and U. rigida, among the 110 strains analyzed in this study. Altogether, this study represents an important advance in our understanding of Ulva biology and provides genetic information for genomic selection of large foliose strains in aquaculture.

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Mitochondrial and chloroplast genome sequences of Ulva ohnoi, a green-tide-forming macroalga in the Southern coastal regions of Japan

Cited by 20 publications

References 26 publications

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

Construction of genomic marker sets based on the chloroplast genome of a green alga, <i>Ulva pertusa</i> (syn. <i>Ulva australis</i>), leads to simple detection of <i>Ulva</i> species

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild

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