Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids

Wang, Xiuliang; Shao, Zhanru; Fu, Wei; Yao, Jianting; Hu, Qian-Nan; Duan, Delin

doi:10.1016/j.margen.2012.12.002

Cited by 28 publications

(20 citation statements)

References 41 publications

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“…The chloroplast genome of S. horneri has a size of 124,068 bp, which is smaller than three other brown algal cpDNAs sequenced to date (Le Corguillé et al 2009;Wang et al 2013). The S. horneri cpDNA is mapped as a canonical quadripartite structure with two 5436 bp inverted repeat regions (IRs), which divide the circular molecule into a small single-copy region (SSC 39,885 bp) and a large single-copy region (LSC 73,311 bp) (Fig.…”

Section: Genome Featuresmentioning

confidence: 82%

“…The DNA sequence of the complete chloroplast genome of S. horneri was determined by comparison with published sequences for three brown algae (Le Corguillé et al 2009;Wang et al 2013). …”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

“…Although gene order of brown algal cpDNAs are different at the order level (Wang et al 2013), their gene length and identity display high similarity (Supplementary Tables S2 and S3). Gene identities in rRNA and tRNA genes of four brown algae are higher than those in PCGs (Fig.…”

Section: Gene Order and Identitymentioning

confidence: 99%

“…To date, over 40 plastid genomes have been sequenced among stramenopiles. However, only three of them are from brown algae including Fucus vesiculosus (order Fucales), Saccharina japonica (order Laminariales), and Ectocarpus siliculosus (order Ectocarpales) (Le Corguillé et al 2009;Wang et al 2013). The brown algal plastid genomes are Electronic supplementary material The online version of this article (doi:10.1007/s10811-015-0609-2) contains supplementary material, which is available to authorized users.…”

Section: Introductionmentioning

confidence: 99%

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Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

Liu

Pang

2015

J Appl Phycol

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Sargassum horneri (Turner) C. Agardh is an important canopy-forming seaweed native to the northwestern Pacific coast growing in the upper sublittoral zone. In this study, the chloroplast genome of S. horneri was fully sequenced and compared with three other brown algal chloroplast genomes. The S. horneri chloroplast genome is 124,068 bp in size with an inverted repeat of 5436 bp and is slightly smaller than the other three brown algal chloroplast DNAs (cpDNAs). It contains 173 genes, including 6 ribosomal RNA (rRNA) genes, 28 transfer RNA (tRNA) genes, and 139 protein-coding genes (PCGs). The coding sequence constitutes 86.32 % of the S. horneri cpDNA. The total spacer size was found to be reduced to 16,967 bp with an average length of 101.0 bp, which makes the S. horneri cpDNA more compact than the other three brown algal cpDNAs. Sixteen small inverted and nine tandem repeats were detected in S. horneri chloroplast genomes. Two introns in trnL2 and trnW genes were identified with the size of 209 and 90 bp, respectively. Its gene content and order are identical to those of Fucus vesiculosus cpDNA, indicating that the chloroplast genome organization at the level of the order Fucales is highly conserved.

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Section: Genome Featuresmentioning

confidence: 82%

“…The DNA sequence of the complete chloroplast genome of S. horneri was determined by comparison with published sequences for three brown algae (Le Corguillé et al 2009;Wang et al 2013). …”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

Section: Gene Order and Identitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

Liu

Pang

2015

J Appl Phycol

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“…To avoid this possibility, the cloned 5S rRNA gene sequence from S. japonica was searched against the kelp chloroplast (GenBank Accession No. JQ405663, Wang et al 2013) and mitochondrion (GenBank Accession No. AP011493, Yotsukura et al 2010) genomic data on NCBI.…”

Section: Discussionmentioning

confidence: 99%

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

et al. 2017

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Nuclear tandemly repeated ribosomal RNA genes (18S-5.8S-25S rDNA and 5S rDNA) have been proven to be excellent cytogenetic markers for karyotype analysis of various higher plants by using the fluorescence in situ hybridization (FISH) technique. To illustrate physical mapping of these rDNAs in brown seaweed, Saccharina japonica, chromosomes, an approximately 5400-bp transcription unit of 18S-5.8S-25S rDNA was assembled by cloning the 25S rDNA after paired-end sequencing of two screened clones from a bacterial artificial chromosome library of kelp gametophytes. In contrast to the conserved 18S-5.8S-25S rDNA and ITS1 in S. japonica, the 245-bp ITS2 was variable in sequence. The cloned 5S rDNA revealed that the 120-bp conserved coding region was separated by a diverse intergenic spacer sequence that were 250, 445, 905, or 1335 bp in length. On average, the 18S-5.8S-25S rDNA of kelp female and male gametophytes had 45 and 41 copies per haploid genome, respectively, as detected by quantitative real-time PCR, whereas the 5S rDNA had 2590 and 2648 copies, respectively. Southern hybridization with labeled probes of 18S rDNA or 5S rDNA demonstrated that kelp gametophytes possessed only one locus each of the 18S-5.8S-25S or 5S rDNAs. This was further confirmed by FISH analysis using the same labeled probes, thus illustrating that 18S-5.8S-25S rDNA is located at the intercalary region of chromosome 23, whereas 5S rDNA at the sub-telomeric region of chromosomes 27. The localization of these rDNAs using the FISH technique has facilitated the identification of individual chromosomes and karyotype analysis of this kelp.

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Loss of a chloroplast encoded function could influence species range in kelp

Rana

Valentin

Bartsch

et al. 2019

Ecology and Evolution

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Kelps are important providers and constituents of marine ecological niches, the coastal kelp forests. Kelp species have differing distribution ranges, but mainly thrive in temperate and arctic regions. Although the principal factors determining biogeographic distribution ranges are known, genomics could provide additional answers to this question. We sequenced DNA from two Laminaria species with contrasting distribution ranges, Laminaria digitata and Laminaria solidungula . Laminaria digitata is found in the Northern Atlantic with a southern boundary in Brittany (France) or Massachusetts (USA) and a northern boundary in the Arctic, whereas L. solidungula is endemic to the Arctic only. From the raw reads of DNA, we reconstructed both chloroplast genomes and annotated them. A concatenated data set of all available brown algae chloroplast sequences was used for the calculation of a robust phylogeny, and sequence variations were analyzed. The two Laminaria chloroplast genomes are collinear to previously analyzed kelp chloroplast genomes with important exceptions. Rearrangements at the inverted repeat regions led to the pseudogenization of ycf 37 in L. solidungula , a gene possibly required under high light conditions. This defunct gene might be one of the reasons why the habitat range of L. solidungula is restricted to lowlight sublittoral sites in the Arctic. The inheritance pattern of single nucleotide polymorphisms suggests incomplete lineage sorting of chloroplast genomes in kelp species. Our analysis of kelp chloroplast genomes shows that not only evolutionary information could be gleaned from sequence data. Concomitantly, those sequences can also tell us something about the ecological conditions which are required for species well‐being.

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Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids

Cited by 28 publications

References 41 publications

Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

Loss of a chloroplast encoded function could influence species range in kelp

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