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Yılmaz E, Mann DG, Gastineau R, Trobajo R, Solak CN, Górecka E, Turmel M, Lemieux C, Ertorun N, Witkowski A. Description of Naviculavanseea sp. nov. (Naviculales, Naviculaceae), a new species of diatom from the highly alkaline Lake Van (Republic of Türkiye) with complete characterisation of its organellar genomes and multigene phylogeny. PHYTOKEYS 2024; 241:27-48. [PMID: 38628637 PMCID: PMC11019260 DOI: 10.3897/phytokeys.241.118903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 04/19/2024]
Abstract
The current article describes Naviculavanseeasp. nov., a new species of diatom from Lake Van, a highly alkaline lake in Eastern Anatolia (Türkiye). The description is based on light and scanning electron microscopy performed on two monoclonal cultures. The complete nuclear rRNA clusters and plastid genomes have been sequenced for these two strains and the complete mitogenome for one of them. The plastome of both strains shows the probable loss of a functional ycf35 gene. They also exhibit two IB4 group I introns in their rrl, each encoding for a putative LAGLIDADG homing endonuclease, with the first L1917 IB4 intron reported amongst diatoms. The Maximum Likelihood phylogeny inferred from a concatenated alignment of 18S, rbcL and psbC distinguishes N.vanseea sp. nov. from the morphologically similar species Naviculacincta and Naviculamicrodigitoradiata.
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Affiliation(s)
- Elif Yılmaz
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - David G. Mann
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Rosa Trobajo
- Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 La Ràpita, Catalunya, Spain
| | - Cüneyt Nadir Solak
- Department of Biology, Faculty of Science & Art, Dumlupınar University, 43000 Kütahya, Türkiye
| | - Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Nesil Ertorun
- Department of Biology, Science Faculty, Eskişehir Technical University, 26000 Eskişehir, Türkiye
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
- Deceased
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Ahmed LT, Alesmail H, Beltran Rodriguez S, Christian R, Coronado J, Elledge AA, Estrada A, Fierro A, Garcia Mora A, Gonzalez K, Gonzalez-Leon S, Guijarro AM, Islas-Quintana J, Juarez-Guido D, Hughey JR, Lara EJ, Lara J, Leonard CT, Lockard KA, Lopez E, Martin S, Martinez M, Mederos B, Medina Pizano A, Medley CJ, Mohsin S, Mumford TF, Muñoz RA, Nachtigall R, Noriega J, Ochoa Cendejas P, Ordaz J, Parra AJ, Pizano J, Reimold M, Rivera K, Rocha A, Rodriguez KC, Tena-Garcia I, Vargas MM, Velasquez J. Complete chloroplast genome of the marine red alga Rhodochorton tenue (Rhodochortonaceae, Rhodophyta) from San Juan Island, Washington. Microbiol Resour Announc 2024; 13:e0106823. [PMID: 38289055 PMCID: PMC10868208 DOI: 10.1128/mra.01068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
We present the complete chloroplast genome sequence of Rhodochorton tenue from San Juan Island, Washington. The chloroplast genome of R. tenue is 192,037 bp in length, contains 244 genes, and is similar in content to Acrochaetium secundatum. Rhodochorton tenue is genetically distinct from Rhodochorton purpureum from the North Atlantic Ocean.
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Affiliation(s)
- Layla T. Ahmed
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Hiba Alesmail
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | | | - Rachel Christian
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jonathan Coronado
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alice A. Elledge
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - America Estrada
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alena Fierro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Angel Garcia Mora
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kayla Gonzalez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Samantha Gonzalez-Leon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Arely M. Guijarro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jennifer Islas-Quintana
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - David Juarez-Guido
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Edward J. Lara
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jamileth Lara
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Carson T. Leonard
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kaylee A. Lockard
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Enzou Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Stephanie Martin
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Miriam Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Brianna Mederos
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alejandro Medina Pizano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Casey J. Medley
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Sarah Mohsin
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Thomas F. Mumford
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, USA
| | - Raphael Araujo Muñoz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Renee Nachtigall
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jannette Noriega
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Pedro Ochoa Cendejas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jessika Ordaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alberto J. Parra
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Julian Pizano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Michelle Reimold
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kristalyn Rivera
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Ayleen Rocha
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Karolina C. Rodriguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Ivan Tena-Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Matthew M. Vargas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jose Velasquez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - On behalf of Hartnell College Genomics Group
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, USA
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Zhao F, Yu CM, Sun HN, Zhao LS, Ding HT, Cao HY, Chen Y, Qin QL, Zhang YZ, Li PY, Chen XL. A novel class of xylanases specifically degrade marine red algal β1,3/1,4-mixed-linkage xylan. J Biol Chem 2023; 299:105116. [PMID: 37524130 PMCID: PMC10470212 DOI: 10.1016/j.jbc.2023.105116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023] Open
Abstract
Xylans are polysaccharides composed of xylose and include β1,4-xylan, β1,3-xylan, and β1,3/1,4-mixed-linkage xylan (MLX). MLX is widely present in marine red algae and constitutes a significant organic carbon in the ocean. Xylanases are hydrolase enzymes that play an important role in xylan degradation. While a variety of β1,4-xylanases and β1,3-xylanases involved in the degradation of β1,4-xylan and β1,3-xylan have been reported, no specific enzyme has yet been identified that degrades MLX. Herein, we report the characterization of a new MLX-specific xylanase from the marine bacterium Polaribacter sp. Q13 which utilizes MLX for growth. The bacterium secretes xylanases to degrade MLX, among which is Xyn26A, an MLX-specific xylanase that shows low sequence similarities (<27%) to β1,3-xylanases in the glycoside hydrolase family 26 (GH26). We show that Xyn26A attacks MLX precisely at β1,4-linkages, following a β1,3-linkage toward the reducing end. We confirm that Xyn26A and its homologs have the same specificity and mode of action on MLX, and thus represent a new xylanase group which we term as MLXases. We further solved the structure of a representative MLXase, AlXyn26A. Structural and biochemical analyses revealed that the specificity of MLXases depends critically on a precisely positioned β1,3-linkage at the -2/-1 subsite. Compared to the GH26 β1,3-xylanases, we found MLXases have evolved a tunnel-shaped cavity that is fine-tuned to specifically recognize and hydrolyze MLX. Overall, this study offers a foremost insight into MLXases, shedding light on the biochemical mechanism of bacterial degradation of MLX.
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Affiliation(s)
- Fang Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chun-Mei Yu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hai-Ning Sun
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Long-Sheng Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hai-Tao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
| | - Hai-Yan Cao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Qi-Long Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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4
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Díaz-Tapia P, Rodríguez-Buján I, Maggs CA, Verbruggen H. Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2023; 59:264-276. [PMID: 36504198 DOI: 10.1111/jpy.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and then reported from other parts of Europe. Conferva parasitica was traditionally included in the genus Pterosiphonia (type species P. cloiophylla in Schmitz and Falkenberg 1897), based on its morphological characters, and later transferred to Symphyocladia and finally to Symphyocladiella using molecular data from an Iberian specimen. However, although morphological differences have been observed between specimens of Symphyocladiella parasitica from northern and southern Europe they have yet to be investigated in a phylogenetic context. In this study, we collected specimens from both regions, studied their morphology and analyzed rbcL and cox1 DNA sequences. We determined the phylogenetic position of a British specimen using a phylogenomic approach based on mitochondrial and plastid genomes. Northern and southern European populations attributed to S. parasitica represent different species. Symphyocladiella arecina sp. nov. is proposed for specimens from southern Europe, but British specimens were resolved as a distant sister lineage to the morphologically distinctive Amplisiphonia, so we propose the new genus Deltalsia for this species. Our study highlights the relevance of using materials collected close to the type localities for taxonomic reassessments, and showcases the utility of genome-based phylogenies for resolving classification issues in the red algae.
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Affiliation(s)
- Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, Paseo Marítimo Alcalde Francisco Vázquez, 10, 15001, A Coruña, Spain
| | - Iván Rodríguez-Buján
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
| | - Christine A Maggs
- Queen's University Marine Laboratory, Portaferry, Newtownards, BT22 1PF, UK
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
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5
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Preuss M, Verbruggen H, West JA, Zuccarello GC. Divergence times and plastid phylogenomics within the intron-rich order Erythropeltales (Compsopogonophyceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2021; 57:1035-1044. [PMID: 33657649 DOI: 10.1111/jpy.13159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
The advent of high-throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient diversifications (subphyla, class) and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopogonophyceae, a group with unusual plastid genomes but with low taxon sampling. We use HTS to produce near complete plastid genomes of all genera, and multiple species within some genera, to produce robust phylogenies to investigate character evolution, dating of divergence in the group, and plastid organization, including intron patterns. Our results produce a fully supported phylogeny of the genera in the Erythropeltales and suggest that morphologies (upright versus crustose) have evolved multiple times. Our dated phylogeny also indicates that the order is very old (~800 Ma), with diversification occurring after the ice ages of the Cryogenian period (750-635 Ma). Plastid gene order is congruent with phylogenetic relationships and suggests that genome architecture does not change often. Our data also highlight the abundance of introns in the plastid genomes of this order. We also produce a nearly complete plastid genome of Tsunamia transpacifica (Stylonematophyceae) to add to the taxon sampling of genomes of this class. The use of plastid genomes clearly produces robust phylogenetic relationships that can be used to infer evolutionary events, and increased taxon sampling, especially in less well-known red algal groups, will provide additional insights into their evolution.
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Affiliation(s)
- Maren Preuss
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - John A West
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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Fang J, Liu B, Liu G, Verbruggen H, Zhu H. Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:780054. [PMID: 34956275 PMCID: PMC8692980 DOI: 10.3389/fpls.2021.780054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 05/17/2023]
Abstract
Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26-36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD -GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.
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Affiliation(s)
- Jiao Fang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Huan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Huan Zhu,
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Liu F, Movahedi A, Yang W, Xu L, Xie J, Zhang Y. The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br. Mol Biol Rep 2020; 47:5013-5024. [PMID: 32515001 DOI: 10.1007/s11033-020-05567-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.
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Affiliation(s)
- Fenxiang Liu
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Wenguo Yang
- Department of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Lei Xu
- Genepioneer Biotechnologies Inc., Nanjing, 210023, China
| | - Jigang Xie
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Yu Zhang
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
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8
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Sumikawa K, Takei K, Kumagai Y, Shimizu T, Yasui H, Kishimura H. In Silico Analysis of ACE Inhibitory Peptides from Chloroplast Proteins of Red Alga Grateloupia asiatica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:391-402. [PMID: 32206928 DOI: 10.1007/s10126-020-09959-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Inhibition of angiotensin I-converting enzyme (ACE) is one of the key factors to repress high blood pressure. Although many studies have been reported that seaweed protein hydrolysates showed the ACE inhibitory activity, the comprehensive understanding of the relationship was still unclear. In this study, we employed chloroplast genome for in silico analysis and compared it with in vitro experiments. We first extracted water-soluble proteins (WSP) from red alga Grateloupia asiatica, which contained mainly PE, PC, APC, and Rbc, and prepared WSP hydrolysate by thermolysin, resulting that the hydrolysate showed ACE inhibitory activity. Then, we determined the complete chloroplast genome of G. asiatica (187,518 bp: 206 protein-coding genes, 29 tRNA, and 3 rRNA) and clarified the amino acid sequences of main WSP, i.e., phycobiliproteins and Rubisco, to perform in silico analysis. Consequently, 190 potential ACE inhibitory peptides existed in the main WSP sequences, and 21 peptides were obtained by in silico thermolysin digestion. By comparing in vitro and in silico analyses, in vitro ACE inhibitory activity was correlated to the IC50 value from in silico digestion. Therefore, in silico approach provides insight into the comprehensive understanding of the potential bioactive peptides from seaweed proteins.
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Affiliation(s)
- Kana Sumikawa
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Kentaro Takei
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Yuya Kumagai
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Takeshi Shimizu
- Department of Research and Development, Hokkaido Industrial Technology Center, Hakodate, Hokkaido, 041-0801, Japan
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan.
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9
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Evans JR, Vis ML. Relative expression analysis of light-harvesting genes in the freshwater alga Lympha mucosa (Batrachospermales, Rhodophyta). JOURNAL OF PHYCOLOGY 2020; 56:540-548. [PMID: 31930498 PMCID: PMC9290634 DOI: 10.1111/jpy.12967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Members of the freshwater red algal order Batrachospermales are often described as shade-adapted. Nevertheless, recent ecophysiological studies have demonstrated species-level differences in acclimation to a range of irradiances. Lympha mucosa occurs in open and shaded portions of temperate streams and is abundant during summer months, suggesting it tolerates high and low irradiances. Specimens of L. mucosa were collected from open (sun-acclimated) or shaded (shade-acclimated) sites and exposed to low (<20 μmol photons · m-2 · s-1 ) or high (220 μmol photon · m-2 · s-1 ) light for 72 h to examine mechanisms of photoacclimation at the transcriptional level. High-throughput sequence data were used to design specific primers for genes involved with light harvesting and these were quantified with qPCR. The greatest significant difference in transcript abundances was observed in the psaA gene (Photosystem I P700 apoprotein), and site-type had an effect on these responses. Shade-acclimated thalli were 22-fold down-regulated at high light, whereas sun-acclimated thalli were only 5-fold down-regulated. Another gene involved with Photosystem I (petF ferredoxin) was down-regulated at high light, but only individuals from the shaded site were significantly different (4-fold). In thalli from both sites, cpeA (Phycoerythrin alpha chain) was down-regulated at high light. Although not statistically significant, patterns consistent with previous physiological and transcriptomic studies were uncovered, namely the inverse response of transcriptional activity in genes that encode phycobiliproteins. In support of previous ecophysiological studies of freshwater red algae, these data indicate significant transcriptional changes involving Photosystem I and phycobiliprotein synthesis are required to tolerate and grow at various irradiances.
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Affiliation(s)
- Joshua R. Evans
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
| | - Morgan L. Vis
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
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10
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Bustamante DE, Hughey JR, Calderon MS, Mansilla A, Rodriguez JP, Mendez F. Analysis of the complete organellar genomes of Palmaria decipiens (Palmariaceae, Rhodophyta) from Antarctica confirms its taxonomic placement in the genus Palmaria. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1734494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Danilo E. Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Martha S. Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
| | - Andres Mansilla
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
| | - Juan P. Rodriguez
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
| | - Fabio Mendez
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
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11
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Zhan SH, Shih C, Liu S. Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era. Ecol Evol 2020; 10:1299-1310. [PMID: 32076515 PMCID: PMC7029088 DOI: 10.1002/ece3.5984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 11/07/2022] Open
Abstract
Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof-of-concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.
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Affiliation(s)
- Shing Hei Zhan
- Department of Zoology & Biodiversity Research Centrethe University of British ColumbiaVancouverBCCanada
| | - Chun‐Chi Shih
- Department of Life Science & Center for Ecology and EnvironmentTunghai UniversityTaichungTaiwan
| | - Shao‐Lun Liu
- Department of Life Science & Center for Ecology and EnvironmentTunghai UniversityTaichungTaiwan
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12
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Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics. Mol Phylogenet Evol 2019; 137:76-85. [PMID: 31029748 DOI: 10.1016/j.ympev.2019.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 11/21/2022]
Abstract
The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative species of the major lineages. Three of the previously recognized families were resolved as independent monophyletic lineages: Ceramiaceae, Wrangeliaceae and Rhodomelaceae. By contrast, our results indicated that the other six families require reclassification. We propose the new order Inkyuleeales, a new circumscription of the Callithamniaceae to include the Spyridiaceae, and a new concept of the Delesseriaceae that includes the Sarcomeniaceae and the Dasyaceae. We also investigated the evolution of the thallus structure, which has been important in the classical delineation of families. The ancestor of the Ceramiales was a monosiphonous filament that evolved into more complex morphologies several times independently during the evolutionary history of this hyperdiverse lineage.
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13
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The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species. Molecules 2019; 24:molecules24020261. [PMID: 30641990 PMCID: PMC6359370 DOI: 10.3390/molecules24020261] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 11/17/2022] Open
Abstract
Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.
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14
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Lee J. Plasmid-Associated Organelle Genome Evolution In Red Algae. JOURNAL OF PHYCOLOGY 2018; 54:772-774. [PMID: 30614001 DOI: 10.1111/jpy.12797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, 16419, Korea
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15
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Iha C, Grassa CJ, Lyra GDM, Davis CC, Verbruggen H, Oliveira MC. Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta). JOURNAL OF PHYCOLOGY 2018; 54:775-787. [PMID: 29989670 DOI: 10.1111/jpy.12765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.
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Affiliation(s)
- Cintia Iha
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher J Grassa
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Goia de M Lyra
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador, Bahia, 40170-115, Brazil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Mariana C Oliveira
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
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16
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Cremen MCM, Leliaert F, West J, Lam DW, Shimada S, Lopez-Bautista JM, Verbruggen H. Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses. Mol Phylogenet Evol 2018; 130:397-405. [PMID: 30227214 DOI: 10.1016/j.ympev.2018.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/04/2018] [Accepted: 09/10/2018] [Indexed: 01/12/2023]
Abstract
The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.
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Affiliation(s)
- Ma Chiela M Cremen
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia.
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium; Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - John West
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Daryl W Lam
- Department of Biological Sciences, The University of Alabama, 35487 AL, USA
| | - Satoshi Shimada
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | | | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia
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17
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Cho CH, Choi JW, Lam DW, Kim KM, Yoon HS. Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats. PLoS One 2018; 13:e0196995. [PMID: 29738547 PMCID: PMC5940233 DOI: 10.1371/journal.pone.0196995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/24/2018] [Indexed: 01/03/2023] Open
Abstract
The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Daryl W. Lam
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
- * E-mail:
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18
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Paiano MO, Del Cortona A, Costa JF, Liu SL, Verbruggen H, De Clerck O, Necchi O. Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta). JOURNAL OF PHYCOLOGY 2018; 54:25-33. [PMID: 29077982 DOI: 10.1111/jpy.12602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.
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Affiliation(s)
- Monica Orlandi Paiano
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, 15054-000, Brazil
| | - Andrea Del Cortona
- Phycology Research Group, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Joana F Costa
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Orlando Necchi
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, 15054-000, Brazil
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19
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Eguiluz M, Yuyama PM, Guzman F, Rodrigues NF, Margis R. Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora. Genet Mol Biol 2017; 40:871-876. [PMID: 29111566 PMCID: PMC5738614 DOI: 10.1590/1678-4685-gmb-2017-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/13/2017] [Indexed: 12/02/2022] Open
Abstract
Plinia trunciflora is a Brazilian native fruit tree from the
Myrtaceae family, also known as jaboticaba. This species has great potential by
its fruit production. Due to the high content of essential oils in their leaves
and of anthocyanins in the fruits, there is also an increasing interest by the
pharmaceutical industry. Nevertheless, there are few studies focusing on its
molecular biology and genetic characterization. We herein report the complete
chloroplast (cp) genome of P. trunciflora using high-throughput
sequencing and compare it to other previously sequenced Myrtaceae genomes. The
cp genome of P. trunciflora is 159,512 bp in size, comprising
inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and
18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding,
30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding
genes demonstrated that P. trunciflora, Eugenia uniflora and
Acca sellowiana form a cluster with closer relationship to
Syzygium cumini than with Eucalyptus. The
complete cp sequence reported here can be used in evolutionary and population
genetics studies, contributing to resolve the complex taxonomy of this species
and fill the gap in genetic characterization.
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Affiliation(s)
- Maria Eguiluz
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Priscila Mary Yuyama
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Frank Guzman
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Nureyev Ferreira Rodrigues
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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20
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Díaz-Tapia P, Maggs CA, West JA, Verbruggen H. Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta). JOURNAL OF PHYCOLOGY 2017; 53:920-937. [PMID: 28561261 DOI: 10.1111/jpy.12553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels.
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Affiliation(s)
- Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole, Dorset, BH12 5BB, UK
| | - Christine A Maggs
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole, Dorset, BH12 5BB, UK
| | - John A West
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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21
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Cabral Oliveira M. Reclassification of the Rhodomelaceae using High Throughput Sequencing: application of big data to algal systematics. JOURNAL OF PHYCOLOGY 2017; 53:917-919. [PMID: 29044565 DOI: 10.1111/jpy.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Mariana Cabral Oliveira
- Botany Department, Institute of Biosciences, University of São Paulo, R. Matão, 277, São Paulo, SP, 05508-090, Brazil
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22
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Verbruggen H, Marcelino VR, Guiry MD, Cremen MCM, Jackson CJ. Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data. JOURNAL OF PHYCOLOGY 2017; 53:790-803. [PMID: 28394415 DOI: 10.1111/jpy.12540] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here, we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically sampled early-branching lineages in the Bryopsidales and Dasycladales respectively. At 80,584 bp, the chloroplast genome of Ostreobium sp. HV05042 is the most compact yet found in the Ulvophyceae. The Avrainvillea chloroplast genome is ~94 kbp and contains introns in infA and cysT that have nearly complete sequence identity except for an open reading frame (ORF) in infA that is not present in cysT. In line with other bryopsidalean species, it also contains regions with possibly bacteria-derived ORFs. The Neomeris data did not assemble into a canonical circular chloroplast genome but a large number of contigs containing fragments of chloroplast genes and showing evidence of long introns and intergenic regions, and the Neomeris chloroplast genome size was estimated to exceed 1.87 Mb. Chloroplast phylogenomics and 18S nrDNA data showed strong support for the Ostreobium lineage being sister to the remaining Bryopsidales. There were differences in branch support when outgroups were varied, but the overall support for the placement of Ostreobium was strong. These results permitted us to validate two suborders and introduce a third, the Ostreobineae.
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Affiliation(s)
- Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Vanessa R Marcelino
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Michael D Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, H91 TK33, Ireland
| | - Ma Chiela M Cremen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher J Jackson
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Nan F, Feng J, Lv J, Liu Q, Fang K, Gong C, Xie S. Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence. Sci Rep 2017; 7:2934. [PMID: 28592899 PMCID: PMC5462760 DOI: 10.1038/s41598-017-03235-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/25/2017] [Indexed: 01/30/2023] Open
Abstract
Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415–484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.
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Affiliation(s)
- Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Kunpeng Fang
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Chaoyan Gong
- School of Life Science, Shanxi University, Taiyuan, (030006), China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, (030006), China.
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Molecular Assisted Identification Reveals Hidden Red Algae Diversity from the Burica Peninsula, Pacific Panama. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9020019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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