The complete chloroplast genome of <i>Saccharina latissima</i>

Fan, Xiao; Xie, Weifeng; Wang, Yitao; Xu, Dong; Zhang, Xiaowen; Ye, Naihao

doi:10.1080/23802359.2020.1825999

Cited by 5 publications

(13 citation statements)

References 7 publications

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“…However, the lack of statistically significant differences in the chloroplast genome as compared with the nuclear genome may partly be explained by the smaller number of genes. The chloroplast genome has a size of 130 kb and contains 139 protein-coding genes, three rRNA genes and 29 tRNA genes (Fan et al 2020b), while the nuclear genome has a size of 545 Mb and contains 18,733 protein-coding genes (Ye et al 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Only methylated sites that were covered in at least one library with coverage >2 were kept in count tables and RPM tables. The sites were annotated for their sequence context (CG or CHG), genomic region, gene ID numbers, and gene functions based on the gff3 annotation file for the S. latissima chloroplast genome from NCBI (Accession: MT151382.1) (Fan et al 2020b).…”

Section: Methodsmentioning

confidence: 99%

“…For an overview of potential methylation sites, and as a backbone to map sequences to the reference chloroplast genome for the S. latissima chloroplast (Fan et al 2020b) was digested in silico using the custom python script InSilicoTypeIIbDigestion_corrected.py (http://marinetics.org/2017/04/11/REdigestions.html) and settings for simulating the restriction enzyme FspEI. The in silico digestion found 270 recognition sites, where 69 were CCGG recognition sites, 61 CCTGG sites, 77 CCTGT sites, and 63 CCAGG sites.…”

Section: In-silico Digestionmentioning

confidence: 99%

“…The chloroplast genome has a size of 130 kb and contains 139 protein-coding genes, three rRNA genes and 29 tRNA genes (Fan et al 2020b), while the nuclear genome has a size of 545…”

Section: Methylation Levels Compared With the Nuclear Genomementioning

confidence: 99%

“…For an overview of potential methylation sites, and as a backbone to map sequences to the reference chloroplast genome for the S. latissima chloroplast (Fan et al 2020b)…”

Section: In-silico Digestionmentioning

confidence: 99%

See 4 more Smart Citations

Chloroplast DNA methylation in the kelpSaccharina latissimais determined by origin and influenced by cultivation

Scheschonk

Nielsen²,

Bischof

et al. 2022

Preprint

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Chloroplast DNA is methylated in the kelp Saccharina japonica, in contrast to most plants. Its function is yet largely unexplored. We detected methylation in the chloroplast DNA of the congener Saccharina latissima, a non – model macroalgal species of high ecological (wild populations) and economical (wild and cultured populations) importance in the North Atlantic. To the functional relevance of chloroplast DNA methylation, we compared for the first time methylation patterns between wild and cultured kelp from different climatic regions (High-Arctic (79 °N) and temperate (53 °N), laboratory samples at 5 °C, 10 °C and 15 °C). Our results suggest genome –wide differences in methylated sites, and methylation level, between the climatic regions. At gene level, our data found functions related to photosynthesis to be the predominant affected case only for differential methylation between origins, but not between growth conditions. Here, sample origin led to significant differences between cultivated and wild samples due to differential methylation of genes related to DNA replication in the Spitsbergen samples. Both findings indicate that origin and cultivation strongly affected the chloroplast methylome, but differently. Similar methylomes for samples from the same origin — independent from whether they grow in the wild or in the lab — suggest that origin– specific methylation marks on the chloroplast genome are inherited. However, the capacity for rapid adaptation (to cultivation conditions) could be shown for Saccharina latissima during this study. Given that DNA – methylation affects gene expression, our study suggests that lab – cultivation alters epigenetically determined kelp chloroplast characteristics at least to the same degree as ecotypic differentiation does.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: In-silico Digestionmentioning

confidence: 99%

“…The chloroplast genome has a size of 130 kb and contains 139 protein-coding genes, three rRNA genes and 29 tRNA genes (Fan et al 2020b), while the nuclear genome has a size of 545…”

Section: Methylation Levels Compared With the Nuclear Genomementioning

confidence: 99%

“…For an overview of potential methylation sites, and as a backbone to map sequences to the reference chloroplast genome for the S. latissima chloroplast (Fan et al 2020b)…”

Section: In-silico Digestionmentioning

confidence: 99%

See 3 more Smart Citations

Chloroplast DNA methylation in the kelpSaccharina latissimais determined by origin and influenced by cultivation

Scheschonk

Nielsen²,

Bischof

et al. 2022

Preprint

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The sugar kelp Saccharina latissima I: recent advances in a changing climate

Diehl,

Li,

Scheschonk

et al. 2023

Annals of Botany

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Background The sugar kelp Saccharina latissima is a Laminariales species widely distributed in the Northern Hemisphere. Its physiology and ecology have been studied since the 1960s, given its ecological relevance on western temperate coasts. However, research interest has been rising recently, driven mainly by reports of negative impacts of anthropogenically induced environmental change and by the increased commercial interest in cultivating the species, with several industrial applications for the resulting biomass. Scope We used a variety of sources published between 2009 to May 2023 (but including some earlier literature where required), to provide a comprehensive review of the ecology, physiology, biochemical and molecular biology of S. latissima. In so doing we aimed to better understand the species’ response to stressors in natural communities, but also inform the sustainable cultivation of the species. Conclusion Due to its wide distribution, S. latissima has developed a variety of physiological and biochemical mechanisms to adjust to environmental changes, including adjustments in photosynthetic parameters, modulation of osmolytes and antioxidants, reprogramming of gene expression and epigenetic modifications, among others summarized in this review. This is particularly important because massive changes in the abundance and distribution of S. latissima have already been observed. Namely, presence and abundance of S. latissima has significantly decreased at the rear edges on both sides of the Atlantic, and increased in abundance at the polar regions. These changes were mainly caused by climate change and will therefore be increasingly evident in the future. Recent developments in genomics, transcriptomics and epigenomics have clarified the existence of genetic differentiation along its distributional range with implications in the fitness at some locations. The complex biotic and abiotic interactions unraveled here demonstrated the cascading effects the disappearance of a kelp forest can have in a marine ecosystem. We show how S. latissima is an excellent model to study acclimation and adaptation to environmental variability and how to predict future distribution and persistence under climate change.

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Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and possibly influenced by cultivation

Scheschonk,

Nilsen,

Bischof

et al. 2024

Evolutionary Applications

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DNA cytosine methylation is an important epigenetic mechanism in genomic DNA. In most land plants, it is absent in the chloroplast DNA. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non‐model macroalgal species of high ecological and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, this fundamental research assessed the chloroplast DNA cytosine methylation in wild and laboratory raised kelp from different climatic origins (High‐Arctic at 79° N, and temperate at 54° N), and in laboratory samples from these origins raised at different temperatures (5, 10 and 15°C). Results suggest genome‐wide differences in methylated sites and methylation level between the origins, while rearing temperature had only weak effects on the chloroplast methylome. Our findings point at the importance of matching conditions to origin in restoration and cultivation processes to be valid even on plastid level.

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The complete chloroplast genome of Saccharina latissima

Cited by 5 publications

References 7 publications

Chloroplast DNA methylation in the kelpSaccharina latissimais determined by origin and influenced by cultivation

Chloroplast DNA methylation in the kelpSaccharina latissimais determined by origin and influenced by cultivation

The sugar kelp Saccharina latissima I: recent advances in a changing climate

Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and possibly influenced by cultivation

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