Mitochondrial genome sequences uncover evolutionary relationships of two Sargassum subgenera, Bactrophycus and Sargassum

Liu, Feng; Li, Xiaodong; Che, Zhiwei

doi:10.1007/s10811-017-1143-1

Cited by 10 publications

(8 citation statements)

References 44 publications

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“…The invasion of such large biomass has had a serious negative impact on the kelp farming and fisheries industries (Liu Feng observation). The Sanya coasts of China have seen hundreds of tons of tropical Sargassum biomass including Sargassum polycystum , Sargassum spinuligerum , Sargassum ilicifolium , and Sargassum aquifolium accumulated along the coasts in spring and seriously affected local tourism as well as the native ecosystems (Liu et al ). Recently, drifting Sargassum biomass was observed in the western Yellow Sea along the Jiangsu coasts from November 2016 to April 2017, a highly unusual sighting along this coastline (Xing et al ).…”

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confidence: 99%

“…One important advantage of organelle genome sequences (mtDNA and ptDNA) over the diploid nuclear genome in Sargassum is that organelle DNA sequences are effectively haploid, with no heterozygosity. This may be the key that will allow for the identification of suitable markers to track the source of a golden tide (Liu et al ). Considering that mtDNAs had an approximately threefold greater mutation rate than ptDNAs in Sargassum species, the mtDNA markers would be more suitable than ptDNA markers for investigating the population genetic diversity (Liu et al ).…”

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confidence: 99%

“…This may be the key that will allow for the identification of suitable markers to track the source of a golden tide . Considering that mtDNAs had an approximately threefold greater mutation rate than ptDNAs in Sargassum species, the mtDNA markers would be more suitable than ptDNA markers for investigating the population genetic diversity (Liu et al 2018).…”

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Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data

Liu

Wang

et al. 2018

Limnology & Oceanography

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Large‐scale drifting Sargassum biomass, known as golden tides, has caused considerable damage to the local environment and economy associated with the Yellow Sea of China. To understand the reoccurrence of Sargassum horneri golden tides in the Yellow Sea, large‐scale spatio‐temporal sampling was performed across nine cruises and five coastal surveys. Morphological data indicated that the floating S. horneri thalli with differing reproductive timing coexisted in the Yellow Sea. A total of 196 S. horneri samples had identical sequences of partial cox3 and rbcL‐S spacer region, revealing very low genetic diversity in the floating biomass. A total of 19 haplotypes for partial cox3 previously found in the Yellow Sea were not detected in our large‐scale sampling. Based on four novel mtDNA markers, the 196 samples could be further distinguished into two forms, which varied in proportions at various locations, but coexisted in each of the spatio‐temporal sampling. These results indicated that the floating Sargassum biomass in the Yellow Sea came from only two dominating haplotypes. The novel findings uncovered by this work will provide further insight into the underlying mechanisms of reoccurring golden tides in the Yellow Sea, and lead to the improved management of the Sargassum biomass.

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Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data

Liu

Wang

et al. 2018

Limnology & Oceanography

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“…The mitogenomes and chloroplast genome contain potential barcodes [67][68][69][70][71][72]. tufA is a genetic marker [16] with higher sensitivity and applicability than ITS, rbcL, universal amplicon, and large ribosomal subunit [18,36,37].…”

Section: Exploration Of the Tufa And Peta Markersmentioning

confidence: 99%

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Cai

Zhao

et al. 2021

PLoS ONE

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Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

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“…The mt and cp genomes of the genus Sargassum have provided important insights into understanding their inter-and intraspecific phylogenetic relationships and evolutionary histories [16,17]. Given uniparental inheritance and accelerated evolutionary rates, mtDNA may provide a higher resolution in elucidating phylogenetic relationships among closely related taxa in brown algae [18].…”

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confidence: 99%

Comparative Analysis of Sequence Polymorphism in Complete Organelle Genomes of the ‘Golden Tide’ Seaweed Sargassum horneri between Korean and Chinese Forms

et al. 2020

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Drifting and inundating brown seaweed Sargassum horneri biomass is called “golden tide”, as it resembles golden massive algal blooms like green tides. This phenomenon occurs globally and its serious ecological impacts on coastal ecosystems have recently begun to be paid attention to. In the present study, by sequencing whole organelle genomes of Korean indigenous S. horneri, we aimed to develop novel molecular markers that can be used for differentiating indigenous from nonindigenous individuals. To this end, we analyzed sequence polymorphisms in mitochondrial (mt) and chloroplast (cp) genomes of two Korean benthic samples in comparison to Chinese ones as a reference. We mapped mt genomes of 34,620~34,628 bp and cp genomes of 123,982~124,053 bp for the Korean samples. In comparative analyses, mtDNA cytochrome c oxidase subunit II (cox2) gene showed the highest number of single nucleotide polymorphisms (SNPs) between Korean and Chinese individuals. NADH dehydrogenase subunit 7 (Nad7)-proline tRNA (trnP) intergenic spacer (IGS) in the mt genome showed a 14 bp insertion or deletion (indel) mutation. For the cp genome, we found a total of 54 SNPs, but its overall evolution rate was approximately four-fold lower than the mt genome. Interestingly, analysis of Ka/Ks ratio in the cp genome revealed a signature of positive selection on several genes, although only negative selection prevalent in mt genome. The ‘candidate’ genetic markers that we found can be applied to discriminate between Korean indigenous and nonindigenous individuals. This study will assist in developing a molecular-based early detection method for effectively managing nonindigenous S. horneri in Korean waters.

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Mitochondrial genome sequences uncover evolutionary relationships of two Sargassum subgenera, Bactrophycus and Sargassum

Cited by 10 publications

References 44 publications

Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data

Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Comparative Analysis of Sequence Polymorphism in Complete Organelle Genomes of the ‘Golden Tide’ Seaweed Sargassum horneri between Korean and Chinese Forms

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