Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment

Wang, Dongmei; Yu, Xinzi; Xu, Kuipeng; Bi, Guoan; Cao, Min; Zelzion, Ehud; Fu, Chunxiang; Sun, Peilong; Liu, Yang; Kong, Fanna; Du, Guoying; Tang, Xiufeng; Yang, Ran; Wang, Junhao; Tang, Lei; Wang, Lu; Zhao, Yingjun; Ge, Yuan; Zhuang, Yunyun; Mo, Zhaolan; Chen, Yu; Gao, Tian; Guan, Xiaowei; Chen, Rui; Qu, Weihua; Sun, Bin; Bhattacharya, Debashish; Mao, Yunxiang

doi:10.1038/s41467-020-17689-1

Cited by 72 publications

(98 citation statements)

References 63 publications

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“…The reference nuclear genome data of P. yezoensis [48] were downloaded from the National Center for Biotechnology Information (NCBI; Assembly number: GCA_009829735.1 ASM982973v1). The reference genome sequence of chloroplast was the assembled sequence of Pyr_1, one of the P. yezoensis samples used in this study.…”

Section: Methodsmentioning

confidence: 99%

Genomic diversity of 39 samples ofPyropiaspecies grown in Japan

Nagano

Kimura

Kobayashi

et al. 2020

Preprint

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8Pyropia species, such as nori (P. yezoensis), are important marine crops. We analysed the genome 9 sequences of 39 Pyropia species grown in Japan. Analysis of organellar genomes showed that the 10 chloroplast and mitochondrial genomes of P. yezoensis have different evolutionary histories. The 11 genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. 12 yezoensis. Nuclear genome analysis revealed nearly 90% of the analysed loci as allodiploid in the 13 hybrid between P. yezoensis and P. tenera. Although the genetic diversity of Japanese P. yezoensis is 14 low, analysis of nuclear genomes genetically separated each accession. Accessions isolated from the 15 sea were often genetically similar to those being farmed. Study of genetic heterogeneity within a single 16 strain of P. yezoensis showed that accessions with frequent abnormal budding formed a single, 17 genetically similar group. The results will be useful for breeding and the conservation of Pyropia 18 species. 19 20In this study, we conducted a phylogenetic analysis of 39 Pyropia accessions grown in Japan using 46 chloroplast DNA sequences assembled from short reads. We also used whole-genome resequencing to 47 analyse the nuclear genomes of 34 accessions of P. yezoensis, one accession of the closely related P. 48 tenera, and one hybrid between P. yezoensis and P. tenera. Particularly, we focused on the analysis of 49 some kinds of seaweed in the Ariake sound, Japan, where seaweed production is the most active. 50 51Results 52Samples used in this study 53 Table 1 summarises the samples used in this study, and Figure 1 shows the isolation site of each 54 sample. In addition to 34 accessions of P. yezoensis, we used P. haitanensis, P. dentata Kjellman, P. 55 tenuipedalis Miura, P. tenera, and the hybrid between P. yezoensis and P. tenera in this study. Many 56 are pure accessions because they were cultured from a monospore (a single haploid cell). 57 58 Chloroplast and mitochondrial genomes 59To elucidate the relationships among the 39 accessions, we analysed their chloroplast DNA 60 sequences. Using the GetOrganelle 31 program, which is a toolkit for assembling the organelle genome 61 from short reads, we attempted to determine the whole chloroplast DNA sequences. Of the 39 total 62 cases, we successfully assembled the whole chloroplast genome of 30 samples, and 9 cases (Pyr_16, 63Pyr_18, Pyr_21, Pyr_29, Pyr_23, Pyr_25, Pyr_28, Pyr_33, and Pyr_34) were unsuccessful. The 64 chloroplast genomes of Pyropia species contain two direct repeats carrying ribosomal RNA (rRNA) 65 operon copies. 26 The circular chloroplast genome has a large single-copy section and a short single-66 copy section between two rRNA repeats. Mapping of the short reads to the assembled chloroplast 67 genome detected two types of reads in the rRNA operons ( Supplementary Figure 1) in all 39 cases, 68reflecting the presence of two non-identical direct repeats carrying two different rRNA operons. 26 The 69 presence of two types of reads in the rRN...

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Section: Methodsmentioning

confidence: 99%

Genomic diversity of 39 samples ofPyropiaspecies grown in Japan

Nagano

Kimura

Kobayashi

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The reference nuclear genome data of P . yezoensis [ 48 ] were downloaded from the National Center for Biotechnology Information (NCBI; Assembly number: GCA_009829735.1 ASM982973v1). The reference genome sequence of chloroplast was the assembled sequence of Pyr_1, one of the P .…”

Section: Methodsmentioning

confidence: 99%

“…The reference nuclear genome data of P. yezoensis [48] were downloaded from the National Center for Biotechnology Information (NCBI; Assembly number: GCA_009829735.1…”

Section: Mapping-based Analysis Of Nuclear Chloroplast and Mitochondrial Genomesmentioning

confidence: 99%

Genomic diversity of 39 samples of Pyropia species grown in Japan

et al. 2021

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Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.

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“…[16,21] Two additional bangiophytes were just sequenced: Pyropia haitanensis [38] and Pyropia yezoensis. [39] Expected outcomes of studies of these genomes and their comparison to others include insights into the attributes needed for multicellularity, stress tolerance, improved understanding of the medically and ecologically important organisms that evolved from endosymbiosis with red algae, and elucidation of the biology of economically relevant foodstuff. In addition, consideration of the genome of Porphyra and comparison to genomes of other red algae, green plants, and animals should provide deep insight into what proteins are necessary for conserved eukaryotic processes and therefore into the mechanisms used to carry out these processes.…”

Section: Red Algal Cell Biology-present State Of Knowledgementioning

confidence: 99%

Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

2021

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The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant.Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells.

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Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment

Cited by 72 publications

References 63 publications

Genomic diversity of 39 samples ofPyropiaspecies grown in Japan

Genomic diversity of 39 samples ofPyropiaspecies grown in Japan

Genomic diversity of 39 samples of Pyropia species grown in Japan

Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

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