1
|
Akita S, Vieira C, Hanyuda T, Rousseau F, Cruaud C, Couloux A, Heesch S, Cock JM, Kawai H. Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences. Mol Phylogenet Evol 2022; 168:107408. [PMID: 35031471 DOI: 10.1016/j.ympev.2022.107408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/16/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022]
Abstract
In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.
Collapse
Affiliation(s)
- Shingo Akita
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan; Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido 041-8611, Japan
| | - Christophe Vieira
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan.
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
| | - Florence Rousseau
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39 75005 Paris, France
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Arnaud Couloux
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Svenja Heesch
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France; Universität Rostock Institut für Biowissenschaften Angewandte Ökologie & Phykologie Albert-Einstein-Straße, 21 18059 Rostock, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
| |
Collapse
|
2
|
Cai C, Gu K, Zhao H, Steinhagen S, He P, Wichard T. Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea. PLoS One 2021; 16:e0250968. [PMID: 34061855 PMCID: PMC8168861 DOI: 10.1371/journal.pone.0250968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/18/2021] [Indexed: 11/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Chuner Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Gu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Hui Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
3
|
Chi S, Wang G, Liu T, Wang X, Liu C, Jin Y, Yin H, Xu X, Yu J. Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:415-429. [PMID: 33248278 PMCID: PMC8242268 DOI: 10.1016/j.gpb.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/20/2018] [Accepted: 12/14/2018] [Indexed: 11/22/2022]
Abstract
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 studied. Our 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 (M1PDH2) and two mannitol-1-phosphatases (M1Pase1 and MIPase2) work together or in combination to exhibit full enzymatic properties. Based on comprehensive transcriptomic data from different tissues, generations, and sexes as well as under different stress conditions, coupled with droplet digital PCR (ddPCR) and proteomic confirmation, we suggest that SjaM1Pase1 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 mechanism. Our proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in Sja. 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 conditions. Our 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.
Collapse
Affiliation(s)
- Shan Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Qingdao Haida BlueTek Biotechnology Co., Ltd., Qingdao 266003, China
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Tao Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Cui Liu
- Qingdao Haida BlueTek Biotechnology Co., Ltd., Qingdao 266003, China
| | - Yuemei Jin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongxin Yin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xin Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
4
|
Choi JW, Graf L, Peters AF, Cock JM, Nishitsuji K, Arimoto A, Shoguchi E, Nagasato C, Choi CG, Yoon HS. Organelle inheritance and genome architecture variation in isogamous brown algae. Sci Rep 2020; 10:2048. [PMID: 32029782 PMCID: PMC7005149 DOI: 10.1038/s41598-020-58817-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/26/2019] [Indexed: 11/08/2022] Open
Abstract
Among the brown algal lineages, Ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. In contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. It has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. In contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. To investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDNA) and two mitochondrial genomes (mtDNA) of isogamous species from the Ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDNAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDNAs of oogamous species showed no rearrangements. Our analysis permits the hypothesis that structural rearrangements in ptDNAs may be a consequence of the mode of inheritance.
Collapse
Affiliation(s)
- Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688, Roscoff, France
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University Muroran, 051-0013, Muroran, Hokkaido, Japan
| | - Chang Geun Choi
- Department of Ecological Engineering, Pukyong National University, Busan, 48513, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| |
Collapse
|
5
|
Liu F, Zhang Y, Bi Y, Chen W, Moejes FW. Understanding the Evolution of Mitochondrial Genomes in Phaeophyceae Inferred from Mitogenomes of Ishige okamurae (Ishigeales) and Dictyopteris divaricata (Dictyotales). J Mol Evol 2019; 87:16-26. [PMID: 30604018 DOI: 10.1007/s00239-018-9881-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 12/15/2018] [Indexed: 11/29/2022]
Abstract
To gain further insight into the evolution of mitochondrial genomes (mtDNAs) in Phaeophyceae, the first recorded characterization of an Ishigeophycidae mtDNA from Ishige okamurae (Yendo), and only the second recorded characterization of a Dictyotophycidae mtDNA from Dictyopteris divaricata (Okamura) Okamura are presented in this study. The 35,485 bp I. okamurae mtDNA contained 36 protein-coding genes (PCGs), 22 tRNAs, three rRNAs, and four open reading frames (orfs), and the 32,021 bp D. divaricata mtDNA harbored 35 PCGs, 25 tRNAs, three rRNAs, and three orfs. The A + T content in D. divaricata (61.69%) was the lowest recorded in sequenced brown algal mtDNAs. The I. okamurae mtDNA displayed unique genome features including an elevated start-codon usage bias for GTG, while the organization of D. divaricata mtDNA was identical to that of Dictyota dichotoma. Phylogenetic analysis based on the amino acid sequence dataset of 35 PCGs indicated that I. okamurae (Ishigeophycidae) diverged early from the Fucophycidae-Dictyotophycidae complex, which was confirmed by the comparative analysis of the mitogenome structure. The novel mitogenome data made available by this study have improved our understanding of the evolution, phylogenetics, and genomics of brown algae.
Collapse
Affiliation(s)
- Feng Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, People's Republic of China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, Shandong, People's Republic of China.
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, People's Republic of China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, People's Republic of China
| | - Weizhou Chen
- Marine Biology Institute, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | | |
Collapse
|
6
|
Comparative study on mitogenomes of green tide algae. Genetica 2018; 146:529-540. [PMID: 30377874 DOI: 10.1007/s10709-018-0046-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
Abstract
Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.
Collapse
|
7
|
Chi S, Liu T, Wang X, Wang R, Wang S, Wang G, Shan G, Liu C. Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina. Curr Genet 2018; 64:259-273. [PMID: 28825126 PMCID: PMC5778160 DOI: 10.1007/s00294-017-0733-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/08/2017] [Accepted: 08/08/2017] [Indexed: 11/26/2022]
Abstract
Although alginate and fucoidan are unique cellular components and have important biological significance in brown algae, and many possible involved genes are present in brown algal genomes, their functions and regulatory mechanisms have not been fully revealed. Both polysaccharides may play important roles in the evolution of multicellular brown algae, but specific and in-depth studies are still limited. In this study, a functional genomics analysis of alginate and fucoidan biosynthesis routes was conducted in Saccharina, and the key events in these pathways in brown algae were identified. First, genes from different sources, including eukaryotic hosts via endosymbiotic gene transfer and bacteria via horizontal gene transfer, were combined to build a complete pathway framework. Then, a critical event occurred to drive these pathways to have real function: one of the mannose-6-phosphate isomerase homologs that arose by gene duplication subsequently adopted the function of the mannose-1-phosphate guanylyltransferase (MGP) gene, which was absent in algal genomes. Further, downstream pathway genes proceeded with gene expansions and complex transcriptional mechanisms, which may be conducive to the synthesis of alginate and fucoidan with diverse structures and contents depending on the developmental stage, tissue structure, and environmental conditions. This study revealed the alginate and fucoidan synthesis pathways and all included genes from separate phylogenetic sources in brown algae. Enzyme assays confirmed the function of key genes and led to the determination of a substitute for the missing MPG. All gene families had constitutively expressed member(s) to maintain the basic synthesis; and the gene function differentiation, enzyme characterization and gene expression regulation differences separated brown algae from other algae lineages and were considered to be the major driving forces for sophisticated system evolution of brown algae.
Collapse
Affiliation(s)
- Shan Chi
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
- Qingdao Haida BlueTek Biotechnology Co., Ltd, Qingdao, Shandong Province, People's Republic of China
| | - Tao Liu
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China.
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ren Wang
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
| | - Shanshan Wang
- Ocean University of China, Qingdao, Shandong Province, People's Republic of China
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guangle Shan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Cui Liu
- Qingdao Haida BlueTek Biotechnology Co., Ltd, Qingdao, Shandong Province, People's Republic of China
| |
Collapse
|
8
|
Kim KM, Choi JW, Yoon HS, Jang HS, Hong JW. Complete mitochondrial genome of Sargassum yezoense (Sargassaceae, Phaeophyceae). Mitochondrial DNA B Resour 2018; 3:424-425. [PMID: 33474190 PMCID: PMC7800866 DOI: 10.1080/23802359.2018.1457993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Kyeong Mi Kim
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hyeong Seok Jang
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Ji Won Hong
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| |
Collapse
|
9
|
Graf L, Kim YJ, Cho GY, Miller KA, Yoon HS. Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers. PLoS One 2017; 12:e0187104. [PMID: 29095864 PMCID: PMC5695614 DOI: 10.1371/journal.pone.0187104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/15/2017] [Indexed: 11/29/2022] Open
Abstract
Coccophora langsdorfii (Turner) Greville (Fucales) is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that should be tested in a large survey of populations of C. langsdorfii.
Collapse
Affiliation(s)
- Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Yae Jin Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ga Youn Cho
- National Institute of Biological Resources, Incheon, Korea
| | - Kathy Ann Miller
- University Herbarium, University of California, Berkeley, CA, United States of America
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| |
Collapse
|
10
|
Sun Y, Jiang Q, Yang C, Wang X, Tian F, Wang Y, Ma Y, Ju Z, Huang J, Zhou X, Zhong J, Wang C. Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis. Curr Genet 2015; 62:383-90. [PMID: 26527116 DOI: 10.1007/s00294-015-0531-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
Abstract
Mitochondrial DNA (mtDNA) has been widely used in species identification and genetic diversification. Comparisons among mtDNAs of closely related species are valuable for phylogenetic studies. However, only the partial mtDNA Cytb gene and the D-loop sequences were used to analysis the phylogenetic relationship between donkey breeds due to lack of complete mitochondrial genome. Dezhou donkey, as a bigger somatotype ass, is one of Chinese domestic donkey breeds, and used by many places as breeding stock. To further investigate the phylogenetic relationship of Dezhou donkey with other breeds, the complete mtDNA was firstly sequenced and de novo assembled using next generation sequence data from total genomic DNA. The genome was 16,813 bp in length (NCBI submission number: KT182635) and contained 13 protein coding genes, 2 ribosomal RNA genes, 25 transfer RNA genes, and 1 control region. Based on the novel complete mtDNA sequence, the sequences of 13 protein coding genes and 2 ribosomal RNA genes were amplifying in other 2 Dezhou donkeys and 3 Yunnan donkeys, respectively. The pattern of genetic variation in horse, wild ass and domestic donkeys among these 15 genes indicated the sequence polymorphisms. The more accurate phylogenetic relationships of donkey species (Dezhou donkey, Yunnan donkey and previously published donkeys) were first obtained using the combined sequences of 12S rRNA+16S rRNA+13 protein-coding genes. Molecular-based phylogeny supported the hypothesis that Chinese domestic donkey breeds may have originated from Somali wild ass, not from Asian wild ass by analyzing mitochondrial genomes.
Collapse
Affiliation(s)
- Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Fang Tian
- Dong E E Jiao Co., Ltd, Dong E County, 252201, China
| | - Yinchao Wang
- Dong E E Jiao Co., Ltd, Dong E County, 252201, China
| | - Yong Ma
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | | | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, No. 159 Industry North Road, Jinan, Shandong, 250131, People's Republic of China.
| |
Collapse
|