From 1a6ccf575ffda3d2d7bd7d98bf07fe826a2f09b7 Mon Sep 17 00:00:00 2001 From: ggserver Date: Wed, 12 Mar 2025 16:59:38 +0000 Subject: [PATCH] Add updates up until 2025-03-12 16:54:34 --- .../87/03ED879475734C73FF2CFF62B1D4856E.xml | 616 ++++++++++++++++++ .../87/03ED879475764C7DFF2CFAFDB698831F.xml | 297 +++++++++ 2 files changed, 913 insertions(+) create mode 100644 data/03/ED/87/03ED879475734C73FF2CFF62B1D4856E.xml create mode 100644 data/03/ED/87/03ED879475764C7DFF2CFAFDB698831F.xml diff --git a/data/03/ED/87/03ED879475734C73FF2CFF62B1D4856E.xml b/data/03/ED/87/03ED879475734C73FF2CFF62B1D4856E.xml new file mode 100644 index 00000000000..19abd475b0c --- /dev/null +++ b/data/03/ED/87/03ED879475734C73FF2CFF62B1D4856E.xml @@ -0,0 +1,616 @@ + + + +Morphology and molecular phylogeny of a Chinese population of Rubrioxytricha guamensis Kumar et al., 2018 (Ciliophora: Hypotrichia) + + + +Author + +Kouser, Farzana +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + + + +Author + +Liao, Lijian +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + + + +Author + +Hu, Xiaozhong +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + +text + + +Journal of Natural History + + +2024 + +2024-06-24 + + +58 + + +21 - 24 + + +688 +701 + + + + +http://dx.doi.org/10.1080/00222933.2024.2361963 + +journal article +10.1080/00222933.2024.2361963 +1464-5262 +13219667 + + + + + + +Morphology of Chinese population of + +Rubrioxytricha guamensis + + + + + + + +Body size highly variable in long-term cultures, 60–125 × 20–35 μm (n = 15) in vivo and 61–186 × 20–63 μm (n = 48) after protargol staining, on average 109 × 32 μm ( +Table 1 +). Body flexible and not contractile, generally long elliptical in outline, both anterior and posterior ends rounded and both margins slightly convex; ratio of length to width 2–5:1 and dorsoventrally flattened about 2:1 ( +Figure 1A,K,L +). Buccal field broad, about half body width; adoral zone occupying approximately 35% of body length in live cells with cilia of membranelles at apical part about 11 μm long ( +Figure 1A,B,K,M,O +). Cortical granules spherical, about 0.5 μm across, yellowish to greenish, arranged in lines or small groups and then in long lines on both ventral and dorsal sides ( +Figure 1D,E +). Cytoplasm colourless with numerous irregular granules 0.5 μm across and food vacuoles containing diatoms and bacteria, which render cells yellow-brown at low magnification. Single contractile vacuole located at the left margin of the body and near mid-body, 12 μm in diameter and the contraction circle is 20s ( +Figure 1A,J +). Two macronuclear nodules, positioned in the middle portion of body and more or less left of midline, with the anterior one close to the buccal vertex, elongate ellipsoidal, on average 16 × 6 μm after protargol preparations ( +Figure 1A,C,I,M +). We did not recognize micronuclei in either live observation or protargol staining. Locomotion is by slowly crawling on the substrate or swimming forward by rotating around the longitudinal axis of the body. + + +Adoral zone composed of 23–35 membranelles ( +Figure 1A,B,F,K,M,O +; +Table 1 +). Undulating membranes in + +Australocirrus + +pattern, at the midline of the body, distinctly curved, paroral membrane extending slightly anterior to endoral membrane and almost equal in length, the two membranes optically intersecting at middle of paroral, cilia about 5 μm long. Eighteen frontal-ventral-transverse (FVT) cirri: three slightly enlarged frontal cirri with the right one close to the distal end of the adoral zone of membranelle; four frontoventral cirri arranged in a V-shaped pattern; single buccal cirrus near the intersection of undulating membranes; five ventral cirri distributed in two groups: three postoral ventral cirri and two pretransverse ventral cirri; five slightly enlarged transverse cirri, about 20 μm long and protruding distinctly behind the rear end of the body in vivo, arranged in a hooked pattern ( +Figure 1B,M,O–Q +). One left and one right marginal cirral row with 16–35 and 17–34 cirri, respectively; rows confluent posteriorly. + + + +Table 1. +Morphological characteristics of the Chinese population of + +Rubrioxytricha guamensis + +. Data based on protargol-stained specimens. Measurements in µm. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CharacterMinMaxMeanMSDCV +n +
Body length61186109.010530.7528.248
Body width206332.4319.9430.748
Adoral zone of membranelles, length205836.3357.6021.048
Adoral membranelles, number233528.7292.89.948
Buccal cirrus, number11110048
Frontal cirri, number33330048
Frontoventral cirri, number44440048
Postoral ventral cirri, number33330048
Pretransverse ventral cirri, number22220048
Transverse cirri, number55550048
Caudal cirrus, number11110048
Left marginal cirri, number163527.0283.8714.448
Right marginal cirri, number173425254.1716.748
Dorsal kineties, number44440048
Dikinetids in DK1, number82013.6142.6519.548
Dikinetids in DK2, number82414.0153.2022.948
Dikinetids in DK3, number82112.9132.9823.148
Dikinetids in DK4, number72012.8133.2225.248
Macronuclear nodules, number22220048
Macronuclear nodule, length92916.1154.9831.048
Macronuclear nodule, width496.461.4422.748
+ + + +Abbreviations:CV,coefficient of variation in %; DK, dorsal kinety; Max,maximum; Mean, arithmetic mean; Min, minimum; +n +, number of cells measured; SD, standard deviation. + + + + +Figure 1. +(A–R) Morphology of Chinese population of +Rubrioxytricha guamensis +from life (A, D–L) and after protargol staining (B, C, M–R). (A) Ventral view of a representative individual. (B, C) Ventral (B) and dorsal (C) view of the same specimen showing the ciliary pattern and nuclear apparatus, arrowhead shows buccal cirrus. (D) Distribution of cortical granules (arrowheads). (E) Shows flexibility of the body; arrowheads represent the spherical yellow cortical granules at the body margin. (F) Ventral view of anterior cell part. (G) Posterior cell part, arrow shows the slightly enlarged transverse cirri. (H) Various cytoplasmic inclusions, ie crystals, lipid droplets. (I) Mid-portion of a slightly squeezed cell, arrows show two macronuclear nodules. (J) Arrow marks the contractile vacuole. (K, L) Ventral views of different cells, showing body shape. (M, N) Ventral (M) and dorsal (N) view of the same specimen, showing ciliature and nuclear apparatus. (O) Ventral view of the anterior end of body. (P) Ventral view of the mid-portion of body, showing left and right marginal rows and postoral ventral cirri. (Q) Ventral view of the posterior portion of cell. (R) Dorsal view of the posterior end of cell, showing caudal cirrus. AZM, adoral zone of membranelles; CC, caudal cirrus; E, endoral membrane; FC, frontal cirri; FVC, frontoventral cirri; LMR, left marginal row; Ma, macronuclear nodules; P, paroral membrane; PTVC, pretransverse ventral cirri; PVC, postoral ventral cirri; RMR, right marginal row; TC, transverse cirri; 1–4, dorsal kineties 1–4. Scale bars = 30 µm. + + + +Invariably, four DK with bristles about 4 μm long in protargol preparations. Kineties almost bipolar with about 14 dikinetids in DK 1 and 2; 13 dikineties in DK 3 and dorsomarginal kinety 4. Single caudal cirrus located at posterior end of DK 3, about 6 μm long in stained cells ( +Figure 1C,N,R +). + + + +18S rRNA gene sequence and phylogenetic analyses ( +Fig. 2 +) + + + +The 18S rRNA gene sequence of + +Rubrioxytricha guamensis + +(excluding both primers) has been deposited in GenBank with accession number PP893155. It has a length of 1657 bp and a G + C content of 45.44%. Phylogenetic trees inferred from the SSU rDNA sequences using BI and ML share similar topologies; therefore, only the ML tree is shown here. All the species of + +Rubrioxytricha + +with data available cluster together within a clade that also includes + +Polystichotrix monilata + +(KT192639) and + +Pseudogastrostyla flava + +(KP266627). Five species of + +Rubrioxytricha + +with data available fall within a well-supported assemblage (ML/ BI, 100%/1.00). The new sequence of + +R. guamensis + +(PP893155) clusters with that of + +R. guamensis + +(KY947508) with high support (ML/BI, 99%/0.86), which is closely related to a cluster including three congeners, + +R. haematoplasma + +(MT364898), + +R. tsinlingensis + +(KR817675) and + +R. ferruginea + +(AF370027). + +Rubrioxytricha guangzhouensis + +(KJ645977) occupies a basal position within the genus. + +Polystichotrix monilata + +(KT192639) and + +Pseudogastrostyla flava + +(KP266627) cluster together with full support (ML/BI, 100%/1.00), which is sister to the + +Rubrioxytricha + +clade (ML/BI, 100%/1.00). These two clades then cluster with + +Ponturostyla enigmatica + +(KC896649) with full support (ML/BI, 100%/1.00). + + + + + +Discussion + + + + +Identification of the Chinese population of +R. guamensis + + + +The genus + +Rubrioxytricha + +comprises six morphospecies, namely + +R. haematoplasma +( +Blatterer and Foissner, 1990 +) +Berger, 1999 + +( +type +species), + +R. guamensis + +Kumar +et al +., 2018a + + +, + +R. ferruginea +( +Stein, 1859 +) +Berger, 1999 + +, + +R. guangzhouensis + +Luo +et al +., 2021 + + +, + +R. indica + +Naqvi +et al +., 2006 + + +, and + +R. tsinlingensis + +Chen +et al +., 2017 + + +, which have all been described in detail (for details, see +Table 2 +). Among them, + +R. guamensis + +can be easily distinguished by the colourless cytoplasm and yellowish cortical granules arranged in short rows and in small groups ( + +Kumar +et al +. 2018a + +). Our population, collected from Qingdao, corresponds well with the +Guam +population of + +R. guamensis + +in terms of ciliature and the colour and arrangement of cortical granules. Nevertheless, the Qingdao population has a relatively larger body length range both in vivo and after protargol staining when compared with the +type +population. We think that geographical variation could account for the abovementioned deviations in body size between the two populations. +Guam +is at a lower latitude than Qingdao and has a higher average annual temperature ( + +Guo +et al +. 2018 + +; + +Yeo +et al +. 2023 + +), and temperature is likely to cause differences in body size between populations of the same species ( + +Kumar +et al +. 2018a + +). The Qingdao population invariably has one caudal cirrus at the end of DK 3, while the +Guam +population sometimes possesses two caudal cirri. Additionally, the +Guam +population was collected from fresh water, while the Qingdao population was isolated from a limnetic biotope with a salinity of about 2‰. However, these divergences could be considered intraspecific variation. + + + + + + +Sequence divergence and phylogenetic position of +Rubrioxytricha guamensis + + + + + + +There are only two nucleotide differences in the 18S rRNA gene between the Qingdao population and the +Guam +population, which corresponds to 99.9% similarity and supports the conspecificity of the two populations. Within the genus, phylogenetic grouping and morphological classification of species are consistent. + +Rubrioxytricha ferruginea + +and + +R. tsinlingensis + +clustered into a branch, which then grouped with + +Rubrioxytricha haematoplasma + +at full confidence level. This can perhaps be explained by the colour of the cytoplasm: all three species have a brown to orange cytoplasm ( +Song and Wilbert 1989 +; +Blatterer and Foissner 1990 +; +Shin and Kim 1993 +; +Berger 1999 +; + +Chen +et al +. 2017 + +; + +Luo +et al +. 2021 + +). The branch of these three species grouped together with the branch consisting of two populations of + +Rubrioxytricha guamensis + +, which may be due to their yellowish to greenish cortical granules ( + +Kumar +et al +. 2018a + +). Independent branching of + +Rubrioxytricha guangzhouensis + +corresponds to its reddish-brown granules. We hypothesise that this may be related to the fact that + +Rubrioxytricha guangzhouensis + +is isolated from marine or brackish water and only + +Rubrioxytricha guangzhouensis + +has mitochondria-like granules. + + + + \ No newline at end of file diff --git a/data/03/ED/87/03ED879475764C7DFF2CFAFDB698831F.xml b/data/03/ED/87/03ED879475764C7DFF2CFAFDB698831F.xml new file mode 100644 index 00000000000..7d5dab89869 --- /dev/null +++ b/data/03/ED/87/03ED879475764C7DFF2CFAFDB698831F.xml @@ -0,0 +1,297 @@ + + + +Morphology and molecular phylogeny of a Chinese population of Rubrioxytricha guamensis Kumar et al., 2018 (Ciliophora: Hypotrichia) + + + +Author + +Kouser, Farzana +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + + + +Author + +Liao, Lijian +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + + + +Author + +Hu, Xiaozhong +College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China; & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China + +text + + +Journal of Natural History + + +2024 + +2024-06-24 + + +58 + + +21 - 24 + + +688 +701 + + + + +http://dx.doi.org/10.1080/00222933.2024.2361963 + +journal article +10.1080/00222933.2024.2361963 +1464-5262 +13219667 + + + + + + +Phylogenetic position of genus +Rubrioxytricha + + + + + + +With the newly sequenced + +Rubrioxytricha guamensis + +included in the phylogenetic analysis, the monophyly of the genus + +Rubrioxytricha + +is corroborated, which is consistent with previous studies ( + +Chen +et al +. 2015 + +, +2017 +; + +Kumar +et al +. 2018a + +). However, + +Luo +et al +. (2021) + +argued for the paraphyly of the genus because of the nesting of + +Pseudogastrostyla flava + +and + +Polystichotrix monilata + +, although it was not statistically supported by the ML (59) analysis. In the current study, the sister relationship between these two species and the genus + +Rubrioxytricha + +is fully supported (ML/BI, 100%/1.00). It can be explained by the high level of morphological similarity among them: they all have a flexible body, one marginal row on each side of the body, and brightly coloured cortical granules. However, + +Rubrioxytricha + +differs significantly from +Polystichothrix +and + +Pseudogastrostyla + +by having a typical oxytrichid pattern of 18 FVT cirri (vs more than 18 FVT cirri in short lines) ( + +Fan +et al +. 2015 + +; + +Luo +et al +. 2017 + +, +2021 +). Furthermore, in terms of dorsal ciliature, the + +Rubrioxytricha +–Polystichothrix– +Pseudogastrostyla + +clade demonstrates great variation: (1) + +Pseudogastrostyla + +shares four DK with + +R. guamensis +, +R. haematoplasma + +and + +R. guangzhouensis + +; (2) +Polystichothrix +shares five DK with + +R. ferruginea + +and + +R. indica + +; (3) six DK are present in + +R. tsinlingensis + +; (4) + +Pseudogastrostyla + +shares one caudal cirrus with + +R. guamensis +, +R. haematoplasma +, +R. indica + +and + +R. guangzhouensis + +; (5) one or two caudal cirri occur in + +R. ferruginea + +and three caudal cirri are present in + +R. tsinlingensis + +; (6) +Polystichothrix +lacks caudal cirri ( +Berger 1999 +; + +Naqvi +et al +. 2006 + +; + +Chen +et al +. 2015 + +; + +Fan +et al +. 2015 + +; + +Luo +et al +. 2017 + +; + +Kumar +et al +. 2018a + +). The branch consisting of species within the genus + +Rubrioxytricha + +and + +Polystichothrix– +Pseudogastrostyla + +is closely related to + +Ponturostyla enigmatica + +and + +Pseudocyrtohymena koreana + +as shown in the previous reports ( + +Chen +et al +. 2017 + +; + +Kumar +et al +. 2018a + +; + +Luo +et al +. 2021 + +). Morphologically, + +Ponturostyla + +differs significantly from the genus + +Rubrioxytricha + +in: (1) having multiple fragmentations (vs absence) of DK 3; (2) more than one (vs one) left and right marginal rows; and (3) absence (vs presence) of caudal cirri ( +Song 2001 +). + +Pseudocyrtohymena + +differs from the genus + +Rubrioxytricha + +in: (1) the arrangement of the undulating membranes (in + +Cyrtohymena + +vs + +Australocirrus + +pattern); and (2) the slightly higher number of adoral membranelles (38–53 vs 21–48) ( + +Jung +et al +. 2015 + +). Thus, the close grouping in phylogenetic analyses might be attributed to the lack of molecular sequences of related species. A detailed investigation of the morphology and the gene sequences of related and yet-tobe-discovered species will clarify further the phylogenetic positions of this group of ciliates. + + + + \ No newline at end of file