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Cho A, Lax G, Keeling PJ. Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages. Mol Phylogenet Evol 2024; 198:108120. [PMID: 38852907 DOI: 10.1016/j.ympev.2024.108120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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2
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Gee CW, Andersen-Ranberg J, Boynton E, Rosen RZ, Jorgens D, Grob P, Holman HYN, Niyogi KK. Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan. Nat Commun 2024; 15:5456. [PMID: 38937455 PMCID: PMC11211512 DOI: 10.1038/s41467-024-49277-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this "red body," focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.
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Affiliation(s)
- Christopher W Gee
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Johan Andersen-Ranberg
- University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg, DK-1871, Denmark
| | - Ethan Boynton
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Rachel Z Rosen
- Department of Chemistry, University of California, Berkeley, CA, 94702, USA
| | - Danielle Jorgens
- Electron Microscope Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Patricia Grob
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- California Institute of Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Hoi-Ying N Holman
- Electron Microscope Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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3
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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024; 60:581-597. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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Barcytė D, Eliáš M. Hydrocytium expands the phylogenetic, morphological, and genomic diversity of the poorly known green algal order Chaetopeltidales. AMERICAN JOURNAL OF BOTANY 2023; 110:e16238. [PMID: 37661934 DOI: 10.1002/ajb2.16238] [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: 06/17/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
PREMISE Chaetopeltidales is a small, understudied order of the green algal class Chlorophyceae, that is slowly expanding with the occasional discoveries of novel algae. Here we demonstrate that hitherto unrecognized chaetopeltidaleans also exist among previously described but neglected and misclassified species. METHODS Strain SAG 40.91 of Characium acuminatum, shown by previous preliminary evidence to have affinities with the orders Oedogoniales, Chaetophorales, and Chaetopeltidales (together constituting the OCC clade), was investigated with light and electron microscopy to characterize its morphology and ultrastructure. Sequence assemblies of the organellar and nuclear genomes were obtained and utilized in bioinformatic and phylogenetic analyses to address the phylogenetic position of the alga and its salient genomic features. RESULTS The characterization of strain SAG 40.91 and a critical literature review led us to reinstate the forgotten genus Hydrocytium A.Braun 1855, with SAG 40.91 representing its type species, Hydrocytium acuminatum. Independent molecular markers converged on placing H. acuminatum as a deeply diverged lineage of the order Chaetopeltidales, formalized as the new family Hydrocytiaceae. Both chloroplast and mitochondrial genomes shared characteristics with other members of Chaetopeltidales and were bloated by repetitive sequences. Notably, the mitochondrial cox2a gene was transferred into the nuclear genome in the H. acuminatum lineage, independently of the same event in Volvocales. The nuclear genome data from H. acuminatum and from another chaetopeltidalean that was reported by others revealed endogenized viral sequences corresponding to novel members of the phylum Nucleocytoviricota. CONCLUSIONS The resurrected genus Hydrocytium expands the known diversity of chaetopeltidalean algae and provides the first glimpse into their virosphere.
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Affiliation(s)
- Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, 710 00, Czech Republic
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, 710 00, Czech Republic
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Temraleeva AD, Portnaya EA. Morphological and Molecular Genetic Analyses of the Genus Vischeria (Eustigmatophyceae, Ochrophyta) in the Algal Collection of Soil Science Institute. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2023; 508:20-31. [PMID: 37186045 DOI: 10.1134/s0012496622700132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 05/17/2023]
Abstract
Four soil eustigmatophyte algal strains isolated from gray forest soils in Moscow and Tula regions of Russia and deposited in the Algal Collection of Soil Science Institute (ACSSI) were examined by morphological and molecular genetic methods. The strains were assigned to the genus Vischeria on evidence of 18S rRNA gene and ITS2 phylogeny. The strains were morphologically similar to V. magna. However, only one of them, ACSSI 026, clustered with the authentic strain SAG 2554, while the other strains formed a separate independent group. The taxonomy of the genus is problematic because its phylogenetic tree based on the 18S rRNA gene and ITS2 is unresolved, the variable regions V4-V5 and V8-V9 of the 18S rRNA gene are noninformative, and the compensatory base change (CBC) concept fails to work (the concept states that closely related species are distinct if even a single CBC occurs in conserved secondary structure regions of ITS2). The concept of species is presumably possible to develop for Eustigmatophyceae and the genus Vischeria in particular when a greater number of eustigmatophyte algal strains are isolated from various biotopes; plastid genes are used or the total plastid genome is deeply sequenced; and ultrastructural, physiological, and biochemical characteristics are studied in more detail.
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Affiliation(s)
- A D Temraleeva
- Institute of Physicochemical and Biological Problems of Soil Sciences, Pushchino Center of Biological Research, Russian Academy of Sciences, Pushchino, Russia.
| | - E A Portnaya
- Institute of Physicochemical and Biological Problems of Soil Sciences, Pushchino Center of Biological Research, Russian Academy of Sciences, Pushchino, Russia
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Barcytė D, Zátopková M, Němcová Y, Richtář M, Yurchenko T, Jaške K, Fawley KP, Škaloud P, Ševčíková T, Fawley MW, Eliáš M. Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae. Mol Phylogenet Evol 2022; 177:107607. [PMID: 35963589 DOI: 10.1016/j.ympev.2022.107607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Eustigmatophyceae is one of the ∼17 classes of the vast algal phylum Ochrophyta. Over the last decade, the eustigmatophytes emerged as an expansive group that has grown from the initially recognized handful of species to well over 200 genetically distinct entities (potential species). Yet the majority of eustigs, remain represented by unidentified strains, or even only metabarcode sequences obtained from environmental samples. Moreover, the formal classification of the group has not yet been harmonized with the recently uncovered diversity and phylogenetic relationships within the class. Here we make a major step towards resolving this issue by addressing the diversity, phylogeny and classification of one of the most prominent eustigmatophyte clades previously informally called the "Eustigmataceae group". We obtained 18S rDNA and rbcL gene sequences from four new strains from the "Eustigmataceae group", and from several additional eustig strains, and performed the most comprehensive phylogenetic analyses of Eustigmatophyceae to date. Our results of these analyses confirm the monophyly of the "Eustigmataceae group" and define its major subclades. We also sequenced plastid genomes of five "Eustigmataceae group" strains to not only improve our understanding of the plastid gene content evolution in eustigs, but also to obtain a robustly resolved eustigmatophyte phylogeny. With this new genomic data, we have solidified the view of the "Eustigmataceae group" as a well-defined family level clade. Crucially, we also have firmly established the genus Chlorobotrys as a member of the "Eustigmataceae group". This new molecular evidence, together with a critical analysis of the literature going back to the 19th century, provided the basis to radically redefine the historical concept of the family Chlorobotryaceae as the formal taxonomic rubric corresponding to the "Eustigmataceae group". With this change, the family names Eustigmataceae and Characiopsidaceae are reduced to synonymy with the Chlorobotryaceae, with the latter having taxonomic priority. We additionally studied in detail the morphology and ultrastructure of two Chlorobotryaceae members, which we describe as Neustupella aerophytica gen. et sp. nov. and Lietzensia polymorpha gen. et sp. nov. Finally, our analyses of partial genomic data from several Chlorobotryaceae representatives identified genes for hallmark flagellar proteins in all of these strains. The presence of the flagellar proteins strongly suggests that zoosporogenesis is a common trait of the family and also occurs in the members never observed to produce flagellated stages. Altogether, our work paints a rich picture of one of the most diverse principal lineages of eustigmatophyte algae.
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Affiliation(s)
- Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
| | - Martina Zátopková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Yvonne Němcová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Michal Richtář
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Tatiana Yurchenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karen P Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marvin W Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
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Rampen SW, Friedl T, Rybalka N, Thiel V. The Long chain Diol Index: A marine palaeotemperature proxy based on eustigmatophyte lipids that records the warmest seasons. Proc Natl Acad Sci U S A 2022; 119:e2116812119. [PMID: 35412908 PMCID: PMC9169758 DOI: 10.1073/pnas.2116812119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/11/2022] [Indexed: 12/23/2022] Open
Abstract
Long chain 1,13- and 1,15-diols are lipids which are omnipresent in marine environments, and the Long chain Diol Index (LDI), based on their distributions, has previously been introduced as a proxy for sea surface temperature. The main biological sources for long chain 1,13- and 1,15-diols have remained unknown, but our combined lipid and 23S ribosomal RNA (23S rRNA) analyses on suspended particulate matter from the Mediterranean Sea demonstrate that these lipids are produced by a marine eustigmatophyte group that originated before the currently known eustigmatophytes diversified. The 18S rRNA data confirm the existence of early-branching marine eustigmatophytes, which occur at a global scale. Differences between LDI records and other paleotemperature proxies are generally attributed to differences between the seasons in which the proxy-related organisms occur. Our results, combined with available LDI data from surface sediments, indicate that the LDI primarily registers temperatures from the warmest month when mixed-layer depths, salinity, and nutrient concentrations are low. The LDI may not be applicable in areas where Proboscia diatoms contribute 1,13-diols, but this can be recognized by enhanced contributions of C28 1,12 diol. Freshwater input may also affect the correlation between temperature and the LDI, but relative C32 1,15-diol abundances help to identify and correct for these effects. When taking those factors into account, the calibration error of the LDI is 2.4 °C. As a well-defined proxy for temperatures of the warmest seasons, the LDI can unlock important and previously inaccessible paleoclimate information and will thereby substantially improve our understanding of past climate conditions.
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Affiliation(s)
- Sebastiaan W. Rampen
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Nataliya Rybalka
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Volker Thiel
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
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Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW. Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae. Genome Biol Evol 2021; 13:6402010. [PMID: 34665222 PMCID: PMC8570151 DOI: 10.1093/gbe/evab233] [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] [Accepted: 10/09/2021] [Indexed: 11/12/2022] Open
Abstract
Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | | | - Xia Xu
- Boyce Thompson Institute, Ithaca, New York, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, USA.,Plant Biology Section, Cornell University, USA
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Fawley MW, Fawley KP, Cahoon AB. Finding needles in a haystack-Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbcL gene using lineage-directed primers. JOURNAL OF PHYCOLOGY 2021; 57:1636-1647. [PMID: 34218435 PMCID: PMC8530920 DOI: 10.1111/jpy.13196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 05/02/2023]
Abstract
Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastid rbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184 rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA-based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species-level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.
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Affiliation(s)
- Marvin W. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - Karen P. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - A. Bruce Cahoon
- Department of Natural Sciences, University of Virginia’s College at Wise, Wise, VA 24293, USA
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