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Wang Y, Liu S, Wang J, Yao Y, Chen Y, Xu Q, Zhao Z, Chen N. Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:749982. [PMID: 35401648 PMCID: PMC8987724 DOI: 10.3389/fpls.2022.749982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000-200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be "super barcodes" for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.
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Affiliation(s)
- Yichao Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shuya Liu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jing Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yanxin Yao
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yang Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qing Xu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zengxia Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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2
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Wu L, Nie L, Guo S, Wang Q, Wu Z, Lin Y, Wang Y, Li B, Gao T, Yao H. Identification of Medicinal Bidens Plants for Quality Control Based on Organelle Genomes. Front Pharmacol 2022; 13:842131. [PMID: 35242042 PMCID: PMC8887618 DOI: 10.3389/fphar.2022.842131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 12/02/2022] Open
Abstract
Bidens plants are annuals or perennials of Asteraceae and usually used as medicinal materials in China. They are difficult to identify by using traditional identification methods because they have similar morphologies and chemical components. Universal DNA barcodes also cannot identify Bidens species effectively. This situation seriously hinders the development of medicinal Bidens plants. Therefore, developing an accurate and effective method for identifying medicinal Bidens plants is urgently needed. The present study aims to use phylogenomic approaches based on organelle genomes to address the confusing relationships of medicinal Bidens plants. Illumina sequencing was used to sequence 12 chloroplast and eight mitochondrial genomes of five species and one variety of Bidens. The complete organelle genomes were assembled, annotated and analysed. Phylogenetic trees were constructed on the basis of the organelle genomes and highly variable regions. The organelle genomes of these Bidens species had a conserved gene content and codon usage. The 12 chloroplast genomes of the Bidens species were 150,489 bp to 151,635 bp in length. The lengths of the eight mitochondrial genomes varied from each other. Bioinformatics analysis revealed the presence of 50–71 simple sequence repeats and 46–181 long repeats in the organelle genomes. By combining the results of mVISTA and nucleotide diversity analyses, seven candidate highly variable regions in the chloroplast genomes were screened for species identification and relationship studies. Comparison with the complete mitochondrial genomes and common protein-coding genes shared by each organelle genome revealed that the complete chloroplast genomes had the highest discriminatory power for Bidens species and thus could be used as a super barcode to authenticate Bidens species accurately. In addition, the screened highly variable region trnS-GGA-rps4 could be also used as a potential specific barcode to identify Bidens species.
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Affiliation(s)
- Liwei Wu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liping Nie
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shiying Guo
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Qing Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhengjun Wu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Yulin Lin
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoli Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Gao
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hui Yao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
- *Correspondence: Hui Yao,
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Liu S, Wang Y, Xu Q, Zhang M, Chen N. Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation. BMC Genomics 2021; 22:746. [PMID: 34654361 PMCID: PMC8520197 DOI: 10.1186/s12864-021-07999-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07999-z.
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Affiliation(s)
- Shuya Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yichao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Qing Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjia Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Nansheng Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Yao Y, Liu F, Chen N. Complete mitochondrial genome of Rhizosolenia setigera (Coscinodiscophyceae, Bacillariophyta). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2319-2321. [PMID: 34291170 PMCID: PMC8279148 DOI: 10.1080/23802359.2021.1950059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rhizosolenia is a species-rich genus with 144 described species, many of which are harmful algal species (HABs) with significant negative ecological impact. Despite their significance in primary production and their potential to induce HABs, genome data of these species remain extremely limited. In this study, the complete mitochondrial genome (mtDNA) of Rhizosolenia setigera Brightwell 1858 was determined for the first time, which also represented the first mtDNA of the order Rhizosoleniales. The circular mtDNA was 34,792 bp in length with GC content of 23.28%. It encoded 63 genes including 35 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 conserved open reading frames (orfs). Phylogenetic analysis using concatenated PCGs revealed that R. setigera and Melosira undulate, which also belongs to the class Coscinodiscophyceae, clustered together as expected. However, comparison of these two mtDNAs revealed extensive genome rearrangement events, suggesting large evolutionary distance. The complete mtDNA of R. setigera will facilitate research on the phylogenetic relationship among Rhizosolenia species, which will in turn facilitate exploration of the evolutionary relationships in the class of Coscinodiscophyceae.
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Affiliation(s)
- Yanxin Yao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,School of Earth and Planetary, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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5
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Zhang M, Cui Z, Liu F, Chen N. Definition of a High-Resolution Molecular Marker for Tracking the Genetic Diversity of the Harmful Algal Species Eucampia zodiacus Through Comparative Analysis of Mitochondrial Genomes. Front Microbiol 2021; 12:631144. [PMID: 33841358 PMCID: PMC8024477 DOI: 10.3389/fmicb.2021.631144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
The cosmopolitan phytoplankton species Eucampia zodiacus is a common harmful algal bloom (HAB) species that have been found to cause HABs in essentially all coastal regions except the Polar regions. However, molecular information for this HAB species is limited with only a few molecular markers. In this project, we constructed the mitochondrial genome (mtDNA) of E. zodiacus, which was also the first mtDNA constructed for any species in the order Hemiaulales that includes 145 reported species (including two additional HAB species Cerataulina bicornis and Cerataulina pelagica). Comparative analysis of eight E. zodiacus strains revealed that they could not be distinguished using common molecular markers, suggesting that common molecular markers do not have adequate resolution for distinguishing E. zodiacus strains. However, these E. zodiacus strains could be distinguished using whole mtDNAs, suggesting the presence of different genotypes due to evolutionary divergence. Through comparative analysis of the mtDNAs of multiple E. zodiacus strains, we identified a new molecular marker ezmt1 that could adequately distinguish different E. zodiacus strains isolated in various coastal regions in China. This molecular marker ezmt1, which was ∼400 bp in size, could be applied to identify causative genotypes during E. zodiacus HABs through tracking the dynamic changes of genetic diversity of E. zodiacus in HABs.
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Affiliation(s)
- Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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6
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Crowell RM, Nienow JA, Cahoon AB. The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica. JOURNAL OF PHYCOLOGY 2019; 55:352-364. [PMID: 30536677 DOI: 10.1111/jpy.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the "dinotom" dinoflagellate Durinskia baltica. A putative strain of N. palea was collected from a pond on the University of Virginia's College at Wise campus and cultured. For initial identification, three markers were sequenced-nuclear 18S rDNA, the chloroplast 23S rDNA, and rbcL. Morphological characteristics were determined using light and scanning electron microscopy; based on these observations the cells were identified as N. palea and named strain "Wise." DNA from N. palea was deep sequenced and the chloroplast and mitochondrial genomes assembled. Single gene phylogenies grouped N. palea-Wise within a clearly defined N. palea clade and showed it was most closely related to the strain "SpainA3." The chloroplast genome of N. palea is 119,447 bp with a quadripartite structure, 135 protein-coding, 28 tRNA, and 3 rRNA genes. The mitochondrial genome is 37,754 bp with a single repeat region as found in other diatom chondriomes, 37 protein-coding, 23 tRNA, and 2 rRNA genes. The chloroplast genomes of N. palea and D. baltica have identical gene content, synteny, and a 92.7% pair-wise sequence similarity with most differences occurring in intergenic regions. The N. palea mitochondrial genome and D. baltica's endosymbiont mitochondrial genome also have identical gene content and order with a sequence similarity of 90.7%. Genome-based phylogenies demonstrated that D. baltica is more similar to N. palea than any other diatom sequence currently available. These data provide the genome sequences of two organelles for a widespread diatom and show they are very similar to those of Durinskia baltica's endosymbiont.
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Affiliation(s)
- Roseanna M Crowell
- Department of Natural Sciences, University of Virginia's College at Wise, Wise, Virginia, 24293, USA
| | - James A Nienow
- Department of Biology, Valdosta State University, Valdosta, Georgia, 31698, USA
| | - Aubrey Bruce Cahoon
- Department of Natural Sciences, University of Virginia's College at Wise, Wise, Virginia, 24293, USA
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7
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Zebrafish-based identification of the antiseizure nucleoside inosine from the marine diatom Skeletonema marinoi. PLoS One 2018; 13:e0196195. [PMID: 29689077 PMCID: PMC5916873 DOI: 10.1371/journal.pone.0196195] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/09/2018] [Indexed: 02/06/2023] Open
Abstract
With the goal of identifying neuroactive secondary metabolites from microalgae, a microscale in vivo zebrafish bioassay for antiseizure activity was used to evaluate bioactivities of the diatom Skeletonema marinoi, which was recently revealed as being a promising source of drug-like small molecules. A freeze-dried culture of S. marinoi was extracted by solvents with increasing polarities (hexane, dichloromethane, methanol and water) and these extracts were screened for anticonvulsant activity using a larval zebrafish epilepsy model with seizures induced by the GABAA antagonist pentylenetetrazole. The methanolic extract of S. marinoi exhibited significant anticonvulsant activity and was chosen for bioassay-guided fractionation, which associated the bioactivity with minor constituents. The key anticonvulsant constituent was identified as the nucleoside inosine, a well-known adenosine receptor agonist with previously reported antiseizure activities in mice and rat epilepsy models, but not reported to date as a bioactive constituent of microalgae. In addition, a UHPLC-HRMS metabolite profiling was used for dereplication of the other constituents of S. marinoi. Structures of the isolated compounds were elucidated by nuclear magnetic resonance and high-resolution spectrometry. These results highlight the potential of zebrafish-based screening and bioassay-guided fractionation to identify neuroactive marine natural products.
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8
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Pogoda CS, Keepers KG, Hamsher SE, Stepanek JG, Kane NC, Kociolek JP. Comparative analysis of the mitochondrial genomes of six newly sequenced diatoms reveals group II introns in the barcoding region of cox1. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29527965 DOI: 10.1080/24701394.2018.1450397] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11. The presence of intronic retrotransposable elements in the barcoding region of cox1 in the Halamphora genomes may explain historic difficulty (especially PCR) with cox1 as a universal barcode for diatoms. Our analysis suggests that high rates of variability in number and position of introns, in many commonly used coding sequences, prevent these from being universally viable as barcodes for diatoms. Therefore, we suggest researchers examine the chloroplast and/or nuclear genomes for universal barcoding markers.
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Affiliation(s)
- Cloe S Pogoda
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Kyle G Keepers
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Sarah E Hamsher
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Joshua G Stepanek
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Nolan C Kane
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - J Patrick Kociolek
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
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9
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Burge DRL, Edlund MB, Frisch D. Paleolimnology and resurrection ecology: The future of reconstructing the past. Evol Appl 2018; 11:42-59. [PMID: 29302271 PMCID: PMC5748527 DOI: 10.1111/eva.12556] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
Paleolimnologists have utilized lake sediment records to understand historical lake and landscape development, timing and magnitude of environmental change at lake, watershed, regional and global scales, and as historical datasets to target watershed and lake management. Resurrection ecologists have long recognized lake sediments as sources of viable propagules ("seed or egg banks") with which to explore questions of community ecology, ecological response, and evolutionary ecology. Most researchers consider Daphnia as the primary model organism in these efforts, but many other aquatic biota, from viruses to macrophytes, similarly produce viable propagules that are incorporated in the sediment record but have been underutilized in resurrection ecology. The common goals shared by these two disciplines have led to mutualistic and synergistic collaborations-a development that must be encouraged to expand. We give an overview of the achievements of paleolimnology and the reconstruction of environmental history of lakes, review the untapped diversity of aquatic organisms that produce dormant propagules, compare Daphnia as a model of resurrection ecology with other organisms amenable to resurrection studies, especially diatoms, and consider new research directions that represent the nexus of these two fields.
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Affiliation(s)
- David R. L. Burge
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
- Water Resources Science Graduate ProgramUniversity of MinnesotaSt. PaulMNUSA
| | - Mark B. Edlund
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
| | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
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10
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Villain A, Kojadinovic M, Puppo C, Prioretti L, Hubert P, Zhang Y, Grégori G, Roulet A, Roques C, Claverie JM, Gontero B, Blanc G. Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. Mitochondrial DNA B Resour 2017; 2:97-98. [PMID: 33490441 PMCID: PMC7800273 DOI: 10.1080/23802359.2017.1285210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9 kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
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Affiliation(s)
- Adrien Villain
- Information Génomique & Structurale UMR 7256, Aix Marseille Univ CNRS, IMM FR 3479, Marseille, France
| | - Mila Kojadinovic
- BIP UMR 7281, IMM FR 3479, Aix Marseille Univ CNRS, Marseille Cedex 20, France
| | - Carine Puppo
- BIP UMR 7281, IMM FR 3479, Aix Marseille Univ CNRS, Marseille Cedex 20, France
| | - Laura Prioretti
- BIP UMR 7281, IMM FR 3479, Aix Marseille Univ CNRS, Marseille Cedex 20, France
| | - Pierre Hubert
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Aix Marseille Univ CNRS UMR 7255 (IMM FR 3479), Marseille, France
| | - Yizhi Zhang
- BIP UMR 7281, IMM FR 3479, Aix Marseille Univ CNRS, Marseille Cedex 20, France
| | - Gérald Grégori
- Mediterranean Institute of Oceanography, Aix Marseille Univ, Univ Toulon, CNRS, Marseille, France
| | - Alain Roulet
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
- UAR1209, INRA, Castanet-Tolosan, France
| | - Céline Roques
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
- UAR1209, INRA, Castanet-Tolosan, France
| | - Jean-Michel Claverie
- Information Génomique & Structurale UMR 7256, Aix Marseille Univ CNRS, IMM FR 3479, Marseille, France
- Assistance Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Brigitte Gontero
- BIP UMR 7281, IMM FR 3479, Aix Marseille Univ CNRS, Marseille Cedex 20, France
| | - Guillaume Blanc
- Information Génomique & Structurale UMR 7256, Aix Marseille Univ CNRS, IMM FR 3479, Marseille, France
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An SM, Noh JH, Lee HR, Choi DH, Lee JH, Yang EC. Complete mitochondrial genome of biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:549-550. [PMID: 33473552 PMCID: PMC7800957 DOI: 10.1080/23802359.2016.1198997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete mitochondrial DNA of biraphid benthic diatom, Navicula ramosissima TA439 was sequenced and characterized. The circular mitogenome contains 67 genes in 48,652 bp (31.1% GC), including 41 protein-coding, 24 transfer RNA (tRNA) and 2 rRNA genes. Twenty-four protein-coding sequences (CDS, 59%) have start with ATG codon and 17 CDS start with alternatives such as ATA (5), ATT (6), TTA (5) and TTG (1). The GC content of tRNA genes (42.1%) is relatively higher than those of the rRNA (35.2%) and CDS (30.5%). Three genes are consisted of multiple exons and introns, i.e. cox1 (three exons, two introns), rps11 (two exons, one intron), rrl (four exons, three introns). Phylogeny of diatoms based on mitogenome data (34 CDS, 8530 amino acids combined) supports the monophyly of Naviculales, including N. ramosissima (Naviculaceae), Berkeleya fennica (Berkeleyaceae), Fistulifera solaris (Stauroneidaceae) and Phaeodactylum tricornutum (Phaeodactylaceae). Mitogenome data may be useful for phylogenetic study of the diatoms and stramenopiles.
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Affiliation(s)
- Sung Min An
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Jae Hoon Noh
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Hyee Ryun Lee
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Dong Han Choi
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Jung Ho Lee
- Department of Biology Education, Daegu University, Gyeongsan, Korea
| | - Eun Chan Yang
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
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