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Molecular phylogeny of diatoms inferred from 18S rDNA sequence using 1704 aligned positions. The tree shown resulted from Bayesian inference using a GTR + I + G model. For clarity, we only show the topology of pennate diatoms. Furthermore, a clade comprising the raphid diatoms and two araphid pennate diatoms Striatella unipunctata/Pseudostriatella oceanica are collapsed into a triangle. Nodal support values (neighbor joining [NJ]/maximum likelihood [ML]/Bayesian inference [BI]) greater than 50 (NJ and ML) and 0.50 (BI) are
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SUMMARYA marine araphid pennate diatom Plagiostriata goreensis is described from the sand grains of Goree Island, Dakar, Republic of Senegal, based on observations of fine structure of its frustule. The most striking feature of the species is its striation, which is angled at approximately 60° across the robust sternum. The other defining features...
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... species of Striatella should be targeted for sequencing to obtain better support for the position of these araphid diatoms. For clarity, we only show the topology of pennate diatoms in Figure 20, excluding the outgroup taxa: bolidomonads and centric diatoms. The original trees containing all analyzed OTUs are available upon request to the first author. ...
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... To date, only two species of Plagiostriata have been described (see Table 1). Species in the genus have a wide distribution, which includes Africa, Europe and Asia (Sato et al. 2009, Li et al. 2018. Additionally, all taxa are restricted to their type localities and show high habitat specificity, i.e. sand sediments but most likely due to their small size and lack of continuity in the collection of samples from beaches in different regions of the world. ...
... In the original description of the genus, the presence of oblique striation (angled at approximately 60° across the sternum) was reported to be one of the main morphological features in Plagiostriata (Sato et al. 2009). This was not observed in P. baltica, which has areolae parallel to the sternum (Li et al. 2018). ...
... The constant features in all species of Plagiostriata are: the reduced rimoportula and simple apical pore fields. (Sato et al. 2009) suggested that the rimoportula could be lost somewhere after the divergence of Plagiostriata at this clade, indicating that the rimoportula is a retained character in Plagiostriata. It is interesting that Plagiostriata (with rimoportula) falls into a clade together with some fragilarioid genera that do not have rimoportula (such as Pseudostaurosira and opephora) (Li et al. 2018). ...
This study describes two new species of Plagiostriata: P. xiapuensis sp. nov. and P. pingtanensis sp. nov., both collected in the intertidal zone of Fujian Province, China. This is the first record of species in the genus Plagiostriata in China. The morphological characteristics of the two new species are discussed in detail using light and scanning electron microscopy. Plagiostriata xiapuensis sp. nov. is characterized by its lower stria density and simple volae-covered areolae compared to the higher stria density, small and complex volae–covered areolae in P. pingtanensis sp. nov. The morphological characteristics of these two species significantly differ from those of P. goreensis and P. baltica in sternum and areolae features, which is also discussed herein.
... But some information available for diatoms in general lays a foundation for understanding the group of araphid diatoms treated here. For example, Cox & Kennaway (2004) and Cox (2010) analysed the origin of the sternum, virgae, vimines, viminules, areolae and associated structures, and the work of Kaluzhnaya & Likhoshway (2007) and Sato et al. (2008Sato et al. ( , 2009Sato et al. ( , 2011 showed how these features arise in the specific case of araphid diatoms. ...
Background and aims-As a result of the description of many new species, reanalyses of type material, and information becoming available on valve morphogenesis in small araphid diatoms lacking a rimoportulae, the existing classification scheme at the genus level needs revision. Because morphological information has increased manyfold since the system provided by Williams & Round (1987), it may now be possible to find distinguishing characters in order to produce a more stable and useful framework, encompassing a morphogenetic perspective, which could then guide the placement of newly discovered taxa. This new framework could also be used to help assess the molecular information generated for the group, based on which many new genera are being erected, but perhaps without proper pondering of morphological data. Methods-A thorough review was made of available published information on the ultrastructure of small-celled araphid diatoms lacking rimoportulae. In addition, image databases were searched, and new light and scanning electron microscopical observations made of some hitherto undescribed species. Key results and conclusions-We provide a table of putative distinguishing features for nine genera (Nanofrustulum, Opephora, Pseudostaurosira, Pseudostaurosiropsis, Punctastriata, Sarcophagodes, Stauroforma, Staurosira and Staurosirella), together with a discussion on their value for discriminating these small diatoms using a morphogenetic perspective. Based on our findings, we amend the genus Pseudostaurosira, establishing wide and short vimines as its most characteristic feature. We use our system in describing a new species from Bolivia, which we place in Nanofrustulum based on its quasifract copulae, the distinguishing trait of the genus. The new species is distinguished from its congeners by its heteropolar valves, apical pore field features, and the multiseriate areolae. We also examine the three genera Popovskayella, Gedaniella, and Serratifera, the latter two recently erected based on molecular information. Since none of these latter genera pass the morphogenetic evaluation we think is essential, we place them in synonymy with other genera and provide the consequent nomenclatural changes. Finally, we make several new combinations in Nanofrustulum, Pseudostaurosira, Sarcophagodes and Staurosirella.
... However, the ultrastructure is instead consistent with the staurosiroid clade of araphid pennate diatoms. These are small-celled araphids [14][15][16] characterized by the presence of a distinct sternum with parallel striae, features considered as synapomorphies of pennates 14,15 , and the absence in general of a labiate process on the valve 14 (Fig. 1). However, these features are not universally conserved across staurosiroids. ...
... However, the ultrastructure is instead consistent with the staurosiroid clade of araphid pennate diatoms. These are small-celled araphids [14][15][16] characterized by the presence of a distinct sternum with parallel striae, features considered as synapomorphies of pennates 14,15 , and the absence in general of a labiate process on the valve 14 (Fig. 1). However, these features are not universally conserved across staurosiroids. ...
Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.
... But some information available for diatoms in general lays a foundation for understanding the group of araphid diatoms treated here. For example, Cox & Kennaway (2004) and Cox (2010) analysed the origin of the sternum, virgae, vimines, viminules, areolae and associated structures, and the work of Kaluzhnaya & Likhoshway (2007) and Sato et al. (2008Sato et al. ( , 2009Sato et al. ( , 2011 showed how these features arise in the specific case of araphid diatoms. ...
Background and aims – As a result of the description of many new species, reanalyses of type material, and information becoming available on valve morphogenesis in small araphid diatoms lacking a rimoportulae, the existing classification scheme at the genus level needs revision. Because morphological information has increased manyfold since the system provided by Williams & Round (1987), it may now be possible to find distinguishing characters in order to produce a more stable and useful framework, encompassing a morphogenetic perspective, which could then guide the placement of newly discovered taxa. This new framework could also be used to help assess the molecular information generated for the group, based on which many new genera are being erected, but perhaps without proper pondering of morphological data. Methods – A thorough review was made of available published information on the ultrastructure of small-celled araphid diatoms lacking rimoportulae. In addition, image databases were searched, and new light and scanning electron microscopical observations made of some hitherto undescribed species. Key results and conclusions – We provide a table of putative distinguishing features for nine genera (Nanofrustulum, Opephora, Pseudostaurosira, Pseudostaurosiropsis, Punctastriata, Sarcophagodes, Stauroforma, Staurosira and Staurosirella), together with a discussion on their value for discriminating these small diatoms using a morphogenetic perspective. Based on our findings, we amend the genus Pseudostaurosira, establishing wide and short vimines as its most characteristic feature. We use our system in describing a new species from Bolivia, which we place in Nanofrustulum based on its quasifract copulae, the distinguishing trait of the genus. The new species is distinguished from its congeners by its heteropolar valves, apical pore field features, and the multiseriate areolae. We also examine the three genera Popovskayella, Gedaniella, and Serratifera, the latter two recently erected based on molecular information. Since none of these latter genera pass the morphogenetic evaluation we think is essential, we place them in synonymy with other genera and provide the consequent nomenclatural changes. Finally, we make several new combinations in Nanofrustulum, Pseudostaurosira, Sarcophagodes and Staurosirella.
... With regard to other small celled araphid diatoms, like the Fragilariaceae, molecular data derived from cultures are largely lacking. Only recently, a few small-celled araphid taxa were described combining morphology and molecular data (Sato et al. 2009. There are only two publications concerning the phylogenetic relationships of the small-celled araphid diatoms (Medlin et al. 2008(Medlin et al. , 2012, both of which suggested that Staurosira, Staurosirella, Pseudostaurosira, Punctastriata were non-monophyletic. ...
Dozens of monoclonal cultures of small-celled araphid diatoms from brackish or marine habitats worldwide were analyzed using morphological observations (light and electron microscopy) and molecular data (nuclear-encoded small subunit ribosomal RNA and chloroplast encoded rbcL and psbC). As a result, we established one new genus Gedaniella, distinguished by a shared morphological character (occlusions of branched volae, projecting from the apical sides of the areolae) and some molecular data, including five new species: G. alfred-wegeneri, G. arenaria, G. boltonii, G. panicellus, G. paucistriata and three new combinations: G. flavovirens, G. guenter-grassii and G. mutabilis. Additionally we describe eleven novel species within the existing genus Serratifera: S. andersonii, S. brevis, S. clavata, S. corallina, S. namibica, S. nosybeana, S. parkii, S. punctata, S. rhombica, S. sourniae, S. takanoi and one new combination S. opephoroides. Furthermore, five new taxa or combinations were described within other genera: such as Cratericulifera crinigera, Nanofrustulum wachnickianum, Plagiostriata baltica, Pseudostaurosira madagascariensis and Stauroforma rinceana. Detailed descriptions for established species are also provided: Nanofrustulum shiloi, Opephora pacifica and Pseudostaurosira elliptica. This study strongly suggests that the complete biodiversity of small-celled araphids is still far from known, and many species currently placed in Opephora and Pseudostaurosira need to be further re-investigated.
... a asterionella gracilis (Ay485447) in Shinninghe-Damsté et al. (2004) and Sorhannus (2007) is a Hyalosira species, see CCMP 469 which is the source of this sequence. b The apical slit of Plagiostriata is unique in shape (Sato et al. 2008e). c The lP of Plagiostriata is highly reduced (Sato et al. 2008e). ...
... b The apical slit of Plagiostriata is unique in shape (Sato et al. 2008e). c The lP of Plagiostriata is highly reduced (Sato et al. 2008e). ...
... Septate girdle bands are observed in many lineages of diatoms (see Round et al. 1990 for licmophora, p. 404, tabellaria ehrenberg, p. 398, a raphid diatom diatomella greville, p. 558) so that it may have been acquired independently in each lineage. Some Hyalosira species are more closely related to rhabdonema, whereas the species in Sato's tree and in that of lobban & Ashworth (2014) These taxa are relatively small in cell size with a highly reduced labiate process (Plagiostriata, Sato et al. 2008e) or absent (Nanofrustulum, Round et al. 1999, opephora, Sabbe et al. 1995, Staurosira, Williams & Round 1987. Apical pore fields are narrow. ...
Phylogenies of the diatoms have largely been inferred from SSU rDNA sequences. Because previously published SSU rDNA topologies of araphid pennate diatoms have varied, a supertree was constructed in order to summarize those trees and used to guide further analyses where problems arose. As previously seen with the SSU trees, araphid diatoms were divided into two clades: basal and core araphids. The basal clade is sister to a clade containing other araphids (core) and the raphid diatoms. Several subclades recovered in the supertree did not correspond to current taxonomy in the diatoms but were supported by ecological and/or morphological characters. A phylogeny of diatoms was then estimated using four gene markers, SSU and LSU rDNA, rbcL and psbk (total 4352 bp) with 42 diatom species chosen to resolve problems in the supertree. Two rooting strategies were explored: 1) one bolidomonad as the closest outgroup of the diatoms and, 2) one bolidomonad and more distantly related heterokon-Tophyte outgroups. Two different strategies were employed to analyze the four gene tree with both Maximum Likelihood (ML) and Baysian Inference (BI) methods. In the first strategy, the variable regions of the LSU rDNA and the third codon position of rbcL were recoded into R (A+G) and Y (T+C) because of substitution saturation detected at these positions in these genes. In the second, these regions were not recoded. Tree topologies of pennates were nearly identical in all analyses. Pennates were divided into three major clades, basal araphid, core araphid and raphid diatoms, as shown in the supertree. The four gene trees displayed better resolution and had stronger bootstrap within the subclades than those of the SSU supertree. The divergence time of the pennates with a Bayesian estimation was estimated, allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. The radiation of pennates into three major clades took place in a short period of geological time before their first appearance in the fossil record and earlier than that proposed by other clocks using single genes.
... With regard to other small celled araphid diatoms, like the Fragilariaceae, molecular data derived from cultures are largely lacking. Only recently, a few small-celled araphid taxa were described combining morphology and molecular data (Sato et al. 2009. There are only two publications concerning the phylogenetic relationships of the small-celled araphid diatoms (Medlin et al. 2008(Medlin et al. , 2012, both of which suggested that Staurosira, Staurosirella, Pseudostaurosira, Punctastriata were non-monophyletic. ...
Diatoms are important contributors to the benthic microeukaryote flora. This manuscript lays the foundation for future metagenomic and environmental sequencing projects off coastal China by curating diatom DNA sequences from the Yantai region of the Bohai and Yellow Seas (Northeast China). These studies are based on cultures established from samples collected in different seasons from marine littoral and supralittoral zones in 2013 and 2014. Thirty-six diatom strains were cultured successfully and identification of these clones was determined by light and scanning electron microscopy(LM and SEM) and DNA sequencing of the nuclear-encoded small subunit ribosomal RNA (SSU)and chloroplast-encoded rbcL and psbC genes. The strains primarily represent raphid pennate genera, such as Amphora, Amphora (Oxyamphora), Caloneis, Diploneis, Halamphora, Navicula, Nitzschia, Parlibellus, Pleurosigma, Surirella and Tryblionella. When the DNA markers from these strains were analysed in a multi-gene phylogeny, we found that some clones-particularly within the genera Amphora, Navicula and Nitzschia-show greater than expected genetic diversity despite their very similar morphology and morphometrics. We also compared the molecular and morphological identities of several seemingly ubiquitous marine littoral taxa in the genera Amphora and Nitzschia from the Indian Ocean and Atlantic Ocean, the Red Sea and Adriatic Sea to their Yellow Sea counterparts.
... As for the core araphids clade "B", there are basically two major groups (Fig 1): a clade with rimoportulae including Fragilaria and Synedra, and a clade lacking rimoportulae, including Nanofrustulum, Opephora, Staurosirella and Staurosira (Fig 11A) [10,[15][16][17]. However, other studies have shown taxa with rimoportulae mixed in this clade, such as Fragilariforma sp. in Medlin et al. [18] or Plagiostriata goreensis in Sato et al. [19]. In describing Plagiostriata goreensis, Sato et al. [19] noted that its rimoportulae were highly reduced, lacking the typically internal labiate-shaped morphology, and up to 10% of the valves lacked it entirely. ...
... However, other studies have shown taxa with rimoportulae mixed in this clade, such as Fragilariforma sp. in Medlin et al. [18] or Plagiostriata goreensis in Sato et al. [19]. In describing Plagiostriata goreensis, Sato et al. [19] noted that its rimoportulae were highly reduced, lacking the typically internal labiate-shaped morphology, and up to 10% of the valves lacked it entirely. The loss of rimoportulae as well as the position of Plagiostriata goreensis in the phylogenetic tree [19] suggested that Plagiostriata goreensis re-acquired its rimoportulae independently after the loss of the structure at the root of the clade. ...
... In describing Plagiostriata goreensis, Sato et al. [19] noted that its rimoportulae were highly reduced, lacking the typically internal labiate-shaped morphology, and up to 10% of the valves lacked it entirely. The loss of rimoportulae as well as the position of Plagiostriata goreensis in the phylogenetic tree [19] suggested that Plagiostriata goreensis re-acquired its rimoportulae independently after the loss of the structure at the root of the clade. In our phylogeny (Fig 1) we recovered a sequential divergence of Fragilariforma, then Plagiostriata, suggesting a gradual loss of the rimoportulae. ...
Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies of the Plagiogrammaceae were inferred but included only up to six genera: Plagiogramma, Dimeregramma, Neofragilaria, Talaroneis, Psammogramma and Psammoneis. In this paper, we describe a new plagiogrammoid genus, Orizaformis, obtained from Bohai Sea (China) and present molecular phylogenies of the family based on three and four genes (nuclear-encoded large and small subunit ribosomal RNAs and chloro-plast-encoded rbcL and psbC). Also included in the new phylogenies is Glyphodesmis. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of Talaroneis, Orizaformis and Psammoneis, and the second of Glyphodesmis, Psammogramma, Neofragilaria, Dimeregramma and Plagiogramma. In addition, we describe three new species within established genera: Psammoneis obaidii, which was collected from the Red Sea, Saudi Arabia; and Neofragilaria stilus and Talaroneis biacutifrons from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: Neofragilaria anomala and Neofragilaria lineata. Our observations suggest that the PLOS ONE |
... The pattern is not observed in any other araphid family of the araphid, including Asterionellopsis Round and Asteroplanus Gardner & Crawford (Fragilariophyceae) and Talaroneis Kooistra & De Stefano (Plagiogrammophyceae), in spite of the fact that they often appear as sister to Rhaphoneis and Delphineis in 18S rDNA phy-logenies (e.g. Alverson et al. 2006;Sorhannus 2007;Kooistra et al. 2009;Sato et al. 2009). Although some raphid diatoms, such as Anorthoneis Grunow and Cocconeis Ehrenberg, also display similar striae arrangements (Round et al. 1990;p. ...
The pattern centre in valve morphogenesis is an annulus in centric diatoms or a sternum in pennate diatoms. The genus Rhaphoneis is currently placed within a lineage that diverges at the root of the pennate diatom clade in most molecular phylogenies, and its valves have a unique pattern to their striae, i.e. radiating from both apices, giving the impression that a pattern centre exists at both ends of the valve and virgae (ribs) formation proceeds centripetally. The present study, however, shows that the pattern centre is actually a linear sternum and the formation of virgae proceeds centrifugally, a pattern centre that is commonly found in most araphid diatoms. Thus, the hypothesis that valve morphogenesis based on a linear sternum and perpendicular virgae is a synapomorphy of pennate diatoms is supported. Our study also demonstrates that the pattern of valve formation can be observed by light microscopy with a direct mounting method when the specimen is relatively large, i.e. exceeding approximately 50 µm in valve length. An important advantage of the use of the direct mounting method is that it requires no repeated centrifugation steps for dehydration, steps necessary for observation by a scanning electron microscope, causing the loss and/or collapse of the specimen, particularly with fragile valves in the early stages of development.
... In terms of areolae occlusions, Nanofrustulum is the genus most similar to O. guenter-grassii. As shown by Sato et al. (2009), Nanofrustulum shiloi and Opephora guenter-grassii are sister taxa. Here we describe N. squammatum, the second species in genus Nanofrustulum represented so far by Nanofrustulum shiloi (= Fragilaria shiloi). ...
Kerguelen is a Subantarctic archipelago, far from other islands or continents. Its isolation provides an interesting field of investigation concerning species diversity and the emergence of morphological differentiation, particularly in diatoms (Bacillariophyta). Several surveys using light (LM) and scanning electron (SEM) microscopy yielded more than 20 new species and (possibly) two new genera. Most of the new species are from Navicula s.s. and were the subject of a separate paper. Here we describe six new species of araphid diatoms. A common feature of these taxa is their various degrees of heteropolarity and the ultrastructure of the transapical striae, typical for species of Opephora defined in the broader sense. A detailed analysis of valve ultrastructure reveals data relevant to the classification of these new taxa into the genera Nanofrustulum (N. squammatum), Pseudostaurosira (P. gersondei, P. quasielliptica, P. latesternum and P. versiformae) and Staurosirella (S. poulinii). Their relationships to Opephora s.S., as defined by Round et al. (1990), are also discussed.
