Biochemical systematics of the marine fish family Centrolophidae (Teleostei:Stromateoidei) from Australian waters

1994 ◽  
Vol 45 (7) ◽  
pp. 1157 ◽  
Author(s):  
CJS Bolch ◽  
RD Ward ◽  
PR Last

The phylogenetic relationships of 11 stromateoid species (nine from the Family Centrolophidae and one each from the Nomeidae and Tetragonuridae) were examined by allozyme electrophoresis. Data from 30 loci were used for three phylogenetic analyses. Two phenetic trees were derived: a UPGMA tree derived from Nei's unbiased genetic distance, and a distance-Wagner tree based on modified Rogers' distances. A cladistic analysis, using maximum parsimony, was also carried out with loci as characters and alleles as unordered states. The tree topology of all three analyses showed a high degree of similarity, which increased confidence in the phylogenetic interpretation and generally supported the classical taxonomic theory of centrolophid relationships. The 'hard-spined' centrolophid taxa, including Seriolella, Psenopsis, Schedophilus labyrinthicus and Hyperoglyphe, formed a stable group In all trees. Psenopsis was closely allied to Seriolella in all three analyses, which supports the view that this genus is derived from Seriolella. Centrolophus and Tubbia consistently diverged from the ancestral line of taxa near the base of the tree, so may have diverged from ancestral stock earlier than previously thought. The most striking departure from current taxonomic theory was the wide separation of Schedophilus labyrinthicus and Schedophilus huttoni, indicating that the genus Schedophilus is polyphyletic. A revision of the genus is needed and should include morphological and electrophoretic analyses of all Schedophilus species, with particular reference to the type species S. medusophagus.

Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2186-2193 ◽  
Author(s):  
Mareike Wenning ◽  
Franziska Breitenwieser ◽  
Christopher Huptas ◽  
Etienne Doll ◽  
Benedikt Bächler ◽  
...  

Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family Propionibacteriaceae with Propioniciclava sinopodophylli and Propioniciclava tarda as the closest relatives (94.6 and 93.5 % similarity, respectively). The cell-wall peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid and was of the A1γ type (meso-DAP-direct). The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and three unidentified glycolipids. The quinone system contained predominantly menaquinone MK-9(H4). The G+C content of the genomic DNA of strain VG341T was 67.7 mol%. The whole-cell sugar pattern contained ribose, rhamnose, arabinose and galactose. On the basis of phenotypic and genetic data, eight strains (VG341T, WS4684, WS4769, WS 4882, WS4883, WS4901, WS4902 and WS4904) are proposed to be classified as members of a novel species in a new genus of the family Propionibacteriaceae , for which the name Brevilactibacter flavus gen. nov., sp. nov. is proposed. The type strain is VG341T (=WS4900T=DSM 100885T=LMG 29089T) and seven additional strains are WS4684, WS4769, WS4882, WS4883, WS4901, WS4902 and WS4904. Furthermore, we propose the reclassification of P. sinopodophylli as Brevilactibacter sinopodophylli comb. nov.


MycoKeys ◽  
2020 ◽  
Vol 74 ◽  
pp. 17-74
Author(s):  
Martina Réblová ◽  
Jana Nekvindová ◽  
Jacques Fournier ◽  
Andrew N. Miller

The Chaetosphaeriaceae are a diverse group of pigmented, predominantly phialidic hyphomycetes comprised of several holomorphic genera including Chaetosphaeria, the most prominent genus of the family. Although the morphology of the teleomorphs of the majority of Chaetosphaeria is rather uniform, their associated anamorphs primarily exhibit the variability and evolutionary change observed in the genus. An exception from the morphological monotony among Chaetosphaeria species is a group characterised by scolecosporous, hyaline to light pink, multiseptate, asymmetrical ascospores and a unique three-layered ascomatal wall. Paragaeumannomyces sphaerocellularis, the type species of the genus, exhibits these morphological traits and is compared with similar Chaetosphaeria with craspedodidymum- and chloridium-like synanamorphs. Morphological comparison and phylogenetic analyses of the combined ITS-28S sequences of 35 isolates and vouchers with these characteristics revealed a strongly-supported, morphologically well-delimited clade in the Chaetosphaeriaceae containing 16 species. The generic name Paragaeumannomyces is applied to this monophyletic clade; eight new combinations and five new species, i.e. P. abietinussp. nov., P. eleganssp. nov., P. granulatussp. nov., P. sabinianussp. nov. and P. smokiensissp. nov., are proposed. A key to Paragaeumannomyces is provided. Using morphology, cultivation studies and phylogenetic analyses of ITS and 28S rDNA, two additional new species from freshwater and terrestrial habitats, Codinaea paniculatasp. nov. and Striatosphaeria castaneasp. nov., are described in the family. A codinaea-like anamorph of S. castanea forms conidia with setulae at each end in axenic culture; this feature expands the known morphology of Striatosphaeria. A chaetosphaeria-like teleomorph is experimentally linked to Dendrophoma cytisporoides, a sporodochial hyphomycete and type species of Dendrophoma, for the first time.


Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1179
Author(s):  
Ueric José Borges de Souza ◽  
Luciana Cristina Vitorino ◽  
Layara Alexandre Bessa ◽  
Fabiano Guimarães Silva

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.


1998 ◽  
Vol 88 (8) ◽  
pp. 782-787 ◽  
Author(s):  
Drake C. Stenger ◽  
Jeffrey S. Hall ◽  
Il-Ryong Choi ◽  
Roy French

The complete nucleotide sequence of wheat streak mosaic virus (WSMV) has been determined based on complementary DNA clones derived from the 9,384-nucleotide (nt) RNA of the virus. The genome of WSMV has a 130-nt 5′ leader and 149-nt 3′-untranslated region and is polyadenylated at the 3′ end. WSMV RNA encodes a single polyprotein of 3,035 amino acid residues and has a deduced genome organization typical for a member of the family Potyviridae (5′-P1/HC-Pro/P3/6K1/CI/6K2/VPg-NIa/NIb/CP-3′). Because WSMV shares with ryegrass mosaic virus (RGMV) the biological property of transmission by eriophyid mites, WSMV has been assigned to the genus Rymovirus, of which RGMV is the type species. Phylogenetic analyses were conducted with complete polyprotein or NIb protein sequences of 11 members of the family Potyviridae, including viruses of monocots or dicots and viruses transmitted by aphids, whiteflies, and mites. WSMV and the monocot-infecting, mite-transmitted brome streak mosaic virus (BrSMV) are sister taxa and share a most recent common ancestor with the whitefly-transmitted sweet potato mild mottle virus, the type species of the proposed genus “Ipomovirus.” In contrast, RGMV shares a most recent common ancestor with aphid-transmitted species of the genus Potyvirus. These results indicate that WSMV and BrSMV should be classified within a new genus of the family Potyviridae and should not be considered species of the genus Rymovirus.


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2858-2864 ◽  
Author(s):  
Teresa Lucena ◽  
María A. Ruvira ◽  
Esperanza Garay ◽  
M. Carmen Macián ◽  
David R. Arahal ◽  
...  

Strain R46T, a marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. It is an aerobic chemo-organotrophic, mesophilic and slightly halophilic organism, with complex ionic requirements. Phylogenetic analyses based on the 16S rRNA and gyrB gene sequences showed that strain R46T formed a separate branch within the family Rhodobacteraceae , bearing similarities below 94.7 and 80.3 %, respectively, to any other recognized species. It contained Q10 as the predominant isoprenoid quinone and C18 : 1ω7c/C18 : 1ω6c as the major cellular fatty acid. Phosphatidylglycerol was the only identified polar lipid, although other lipids were also detected. The DNA G+C content of the genomic DNA was 61.3 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the strain represents a novel genus and species, for which the name Actibacterium mucosum gen. nov., sp. nov. is proposed. The type strain of the type species is Actibacterium mucosum R46T ( = CECT 7668T = KCTC 23349T).


Parasitology ◽  
2000 ◽  
Vol 120 (1) ◽  
pp. 45-56 ◽  
Author(s):  
S. MORAND ◽  
C. D. M. MÜLLER-GRAF

Schistosomes, which live as parasitic adults in the blood vessels of mammals, birds and crocodiles, are unique among trematodes because they have separate sexes. Several studies have shown that the sex ratio is often biased towards males. Sexual dimorphism can be very important in several genera (Schistosoma, Heterobilharzia, Schistosomatium), as larger males grip smaller females in a gynecophoric canal. But not all schistomatid species have developed a gynecophoric canal. It is also striking that the number of testes varies widely, from a small number of testes reported (2–7) to a very high number (>500). We tested the hypothesis of trade-off investment by males: muscle (as estimated by the length of the gynecophoric canal) in order to sequester one or a few females, or testes in order to inseminate numerous females. We used recent comparative methods, which need phylogenetic information of the analysed species. We employed a morphological cladistic analysis of the Schistosomatidae and a construction of a phylogenetic supertree of Schistosoma based on available molecular information. Our phylogenetic analysis supports previous hypotheses on the origin and diversification of the schistosomes. The family seems to have originated as parasites of crocodiles (or possibly other related poikilotherms) and to have secondarily evolved within the Aves and then mammals. Our phylogenetic analyses show that (1) the possession of a gynecophoric canal is a plesiomorphic character, and several reductions of this character have occurred during the diversification of the Schistosomatidae; (2) a small number of testes is a plesiomorphic stage, and an increase of testes number has occurred several times. Finally, our comparative analysis suggests that there is a trade-off between investment in muscle or in number of testes (other variables being controlled for). Male competition for access to females seems to follow two ways: investment in testes in order to fertilize a high number of females or investment in muscle in order to hold and sequester one (Schistosoma) or a few females (Heterobilharzia). We show the existence of the trade-off between muscles and testes in connection with a male biased sex ratio. The development of dioecy cannot explain the trade-off between muscles and testes, which instead appears to be a result of sexual selection possibly driven by the male biased sex ratio.


Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.


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