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Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae

Acta Oceanologica Sinica 2018年第4期37卷 89-101页

作者： wang Shanshan ZHANG Lei CHI Shan wang Guoliang wang xumin LIU Tao TANG Xuexi College of Marine Life Sciences Ocean University of China CAS Key Laboratory of Genome Sciences and Information/Beijing Key Laboratory of Genome and Precision Medicine Technologies Beijing Institute of GenomicsChinese Academy of Sciences

Carotenoids play a crucial role in absorbing light energy for photosynthesis,as well as in protecting chlorophyll from *** contrast to the Streptophyta,few studies have examined carotenoid biosynthetic pathways in algae,owing to a shortage of *** part of the 1000 Plants Project,we sequenced and assembled the transcriptomes of 41 marine macroalgal species,including 22 rhodophytes and 19 phaeophytes,and then combined the datasets with publicly available data from Gen Bank（National Center for Biotechnology Information） and the *** of Energy Joint Genome *** a result,we identified 68 and 79 fulllength homologs in the Rhodophyta and Phaeophyceae,respectively,of seven inferred carotenoid biosynthetic genes,including the genes for phytoene synthase（PSY）,phytoene desaturase（PDS）,ζ-carotene desaturase（ZDS）,ζ-carotene isomerase（Z-ISO）,prolycopene isomerase（crt ISO）,lycopene β-cyclase（LCYB）,and lycopene ε-cyclase（LCYE）.We found that the evolutionary history of the algal carotenoid biosynthetic pathway was more complex than that of the same pathway in the Streptophyta and,more specifically,that the evolutionary history involved endosymbiotic gene transfer,gene duplication,and gene *** all of the eukaryotic algae that we examined had inherited the seven carotenoid biosynthesis genes via endosymbiotic gene ***,PSY,crt ISO,and the ancestral lycopene cyclase gene（LCY） underwent duplication events that resulted in multiple gene copies,and the duplication and subsequent divergence of LCYB and LCYE specialized and complicated the cyclization of *** findings also verify that the loss of LCYE in both the microphytic rhodophytes and phaeophytes explains the differences in their carotenoid patterns,when compared to the macrophytic *** analyses provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of caro

关键词： carotenoid biosynthesis algae phylogenetic analysis

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Origin and evolution of alginate-c5-mannuronan-epimerase gene based on transcriptomic analysis of brown algae

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Acta Oceanologica Sinica 2014年第2期33卷 73-85页

作者： wang Ren wang xumin ZHANG Yalan YU Jun LIU Tao CHEN Shengping CHI Shan College of Marine Life Science Ocean University of China CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome andPrecision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChineseAcademy of Sciences Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism Zhong ShanSchool of MedicineSun Yat-Sen University

The coding product of alginate-c5-mannuronan-epimerase gene （algG gene） can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate. Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems. In this article, based on some algal and bacterial algG genes registered on GenBank and EMBL databases, we predicted 94 algG genes open reading frame （ORF） sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project （OneKP）. By method of transcriptomic sequence analysis, gene structure and gene localization analysis, multiple sequence alignment and phylogenetic tree construction, we studied the algal algG gene family characteristics, the structure modeling and conserved motifs of AlgG protein, the origin of alginate biosyn-thesis and the variation incidents that might have happened during evolution in algae. Although there are different members in the algal algG gene family, almost all of them harbor the conserved epimerase region. Based on the phylogenetic analysis of algG genes, we proposed that brown algae acquired the alginate bio-synthesis pathway from an ancient bacterium by horizontal gene transfer （HGT）. Afterwards, followed by duplications, chromosome disorder, mutation or recombination during evolution, brown algal algG genes were divided into different types.

关键词： transcriptomic sequencing alginate-c5-mannuronan-epimerase gene gene family alginate phylogenetic analysis

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Mitochondrial genomes of Tapes dorsatus and Cardita variegata:insights into Heteroconchia phylogeny

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Journal of Oceanology and Limnology 2024年第3期42卷 943-959页

作者： xumin wang Hua ZHANG Xindong TENG Wenhui SUN Zhikai XING Shuang wang Xiumei LIU Jiangyong QU Lijun wang College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China

Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve *** relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between *** the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput *** is the first mitochondrial genome belonging to the family Carditidae to be *** used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of *** results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,*** analysis show that gene arrangement within Venerida was highly ***-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 *** results provide evidence of the internal relationships of Heteroconchia.

关键词： Tapes dorsatus Cardita variegata mitochondrial genome phylogeny

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The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome

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Acta Oceanologica Sinica 2014年第2期33卷 108-113页

作者： FENG Yanjing CHI Shan LIU Cui CHEN Shengping YU Jun wang xumin LIU Tao College of Marine Life Science Ocean University of China Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism Zhong Shan School of MedicineSun Yat-Sen University CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChineseAcademy of Sciences

Phosphomannomutase （PMM;EC 5.***.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project （OneKP） in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.

关键词： transcriptomic sequencing Chromista phosphomannomutase conserved motif phylogenetic analysis

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Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

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Acta Oceanologica Sinica 2024年第2期43卷 137-150页

作者： Jiangyong Qu Wanqi Yang Xindong Teng Li Xu Dachuan Zhang Zhikai Xing Shuang wang Xiumei Liu Lijun wang xumin wang College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China Qingdao Dagang Customs Qingdao 266071China

Caenogastropoda is a highly diverse group,containing~60%of all existing *** in this subclass predominantly inhabit marine environments and have a high ecological and economic *** to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has ***,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain *** the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea *** composition analysis indicated that whole sequences were biased toward A and *** compared them with 171 complete mitochondrial genomes of *** phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close *** study supported Caenogastropoda at the molecular level as a separate clade of *** to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

关键词： mitochondrial genome phylogenetic analysis Caenogastropoda

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Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica

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Genomics, Proteomics & Bioinformatics 2020年第4期18卷 415-429页

作者： Shan Chi Guoliang wang Tao Liu xumin wang Cui Liu Yuemei Jin Hongxin Yin Xin Xu Jun Yu College of Marine Life Sciences Ocean University of ChinaQingdao 266003China Qingdao Haida BlueTek Biotechnology Co. Ltd.Qingdao 266003China CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology Beijing Agro-Biotechnology Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China College of Life Sciences Yantai UniversityYantai 264005China

As a carbon-storage compound and osmoprotectant in brown algae,mannitol is synthesized and then accumulated at high levels in Saccharina japonica(Sja);however,the underlying control mechanisms have not been *** analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps.A mannitol-1-phosphate dehydrogenase(M1 PDH2)and two mannitol-1-phosphatases(M1 Pase1 and MIPase2)work together or in combination to exhibit full enzymatic *** on comprehensive transcriptomic data from different tissues,generations,and sexes as well as under different stress conditions,coupled with droplet digital PCR(dd PCR)and proteomic confirmation,we suggest that Sja M1 Pase1 plays a major role in mannitol biosynthesis and that the basic mannitol anabolism and the carbohydrate pool dynamics are responsible for carbon storage and anti-stress *** proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in *** addition,we discover that mannitol-metabolism-associated(MMA)genes show differential expression between the multicellular filamentous(gametophyte)and large parenchymal thallus(sporophyte)generations and respond differentially to environmental stresses,such as hyposaline and hyperthermia *** results indicate that the ecophysiological significance of such differentially expressed genes may be attributable to the evolution of heteromorphic generations(filamentous and thallus)and environmental adaptation of Laminariales.

关键词： Mannitol metabolism Saccharina japonica RNA-seq Proteomic analyses Biochemical characterization

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Phylogeny of genera Laminaria and Saccharina(Laminariales, Phaeophyceae) based on three molecular markers

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Acta Oceanologica Sinica 2014年第9期33卷 139-151页

作者： CHI Shan QIAN Hao LI Tianyong wang xumin LIU Cui REN Lei TANG Xuexi LIU Tao Ocean University of China Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of Genomics Chinese Academy of Sciences Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine Technologies Beijing Institute of Genomics Chinese Academy of Sciences

In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera： Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Lami- nariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae-Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxi- dase I （COI） sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer （ITS） and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina.

关键词： Saccharina Laminaria phylogeny COI rbcL ITS

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Comparative analysis on transcriptome sequencings of six Sargassum species in China

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Acta Oceanologica Sinica 2014年第2期33卷 37-44页

作者： wang Guoliang SUN Jing LIU Guiming wang Liang YU Jun LIU Tao CHI Shan LIU Cui GUO Haiyan wang xumin WU Shuangxiu CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucle-otides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups （COG）, gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were also performed for further un-derstanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metab-olism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenet-ic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.

关键词： Sargassum Sargassum fusiforme transcriptome sequencing comparative analysis

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Ribogenomics: the Science and Knowledge of RNA

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Genomics, Proteomics & Bioinformatics 2014年第2期12卷 57-63页

作者： Jiayan Wu Jingfa Xiao Zhang Zhang xumin wang Songnian Hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs（mRNAs） are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAembryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.

关键词： RNA Ribogenomics Operational Informational Transcriptome

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Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

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Acta Oceanologica Sinica 2014年第2期33卷 1-12页

作者： WU Shuangxiu SUN Jing CHI Shan wang Liang wang xumin LIU Cui LI Xingang YIN Jinlong LIU Tao YU Jun CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.

关键词： Phaeophyceae brown algae Rhodophyta red algae marine macroalgae transcriptome sequencing secondary generation sequencing

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