scholarly journals Comparative genomics on cultivated and uncultivated, freshwater and marine Candidatus Manganitrophaceae species implies their worldwide reach in manganese chemolithoautotrophy

2021 ◽  
Author(s):  
Hang Yu ◽  
Grayson L Chadwick ◽  
Usha F Lingappa ◽  
Jared Renton Leadbetter
Keyword(s):  
South Africa ◽  
Carbon Fixation ◽  
Comparative Genomic ◽  
Santa Barbara ◽  
Manganese Oxidation ◽  
Species Phylogeny ◽  
Core Set ◽  
The Family ◽  
Genomic Analyses ◽  
A New Species

Chemolithoautotrophic manganese oxidation has long been theorized, but only recently demonstrated in a bacterial co-culture. The majority member of the co-culture, Candidatus Manganitrophus noduliformans, is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO3-oxidizing cultures using inocula from Santa Barbara (USA) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated Candidatus Manganitrophus morganii. The next abundant members differed in the available cultures, suggesting that while Ca. Manganitrophus species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated Ca. Manganitrophus and related metagenome-assembled genomes revealed a coherent taxonomic family, Candidatus Manganitrophaceae, from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse Complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse TCA carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that Ca. Manganitrophaceae share a core set of candidate genes for the newly discovered manganese dependent chemolithoautotrophic lifestyle, and likely have a broad, global distribution.

Cissococcus Cockerell (Hemiptera: Coccoidea: Coccidae), a unique gall-inducing soft scale genus on Vitaceae from South Africa, with description of a new species

Zootaxa ◽  
2011 ◽  
Vol 2996 (1) ◽  
pp. 1 ◽  
Author(s):  
C. J. HODGSON ◽  
I. M. MILLAR ◽  
P. J. GULLAN
Keyword(s):  
South Africa ◽  
Type Species ◽  
Scale Insect ◽  
Instar Nymph ◽  
Closely Related Species ◽  
Soft Scale ◽  
First Instar ◽  
The Family ◽  
Gall Induction ◽  
A New Species

The gall-inducing genus Cissococcus Cockerell is revised to include two species. The family placement of Cissococcus has been uncertain, but characters of the first-instar nymph and adult male clearly show that Cissococcus is a soft scale insect (Coccidae) and is therefore the only member of the Coccidae known to induce a complex covering gall. All stages of the type species, C. fulleri Cockerell, are described and illustrated, plus the adult and third-instar female and first-instar nymph of a new, closely-related species, C. braini Hodgson & Millar sp. n. Both species are known only from wild vines in the southeast and C. fulleri also in the northeast of South Africa, but each induces a unique gall and each appears to be restricted to a different species of Rhoicissus (Vitaceae). The galls of each species are described and figured, and gall induction in the Coccidae is briefly discussed.

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

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.

scholarly journals A review of gorgonian coral species (Cnidaria, Octocorallia, Alcyonacea) held in the Santa Barbara Museum of Natural History research collection: focus on species from Scleraxonia, Holaxonia, Calcaxonia – Part II: Species of Holaxonia, families Gorgoniidae and Plexauridae

ZooKeys ◽  
2019 ◽  
Vol 860 ◽  
pp. 67-182
Author(s):  
Elizabeth Anne Horvath
Keyword(s):  
Systematic Review ◽  
New Species ◽  
Natural History ◽  
Species Identification ◽  
Coral Species ◽  
Santa Barbara ◽  
Gorgonian Coral ◽  
The Family ◽  
Research Collection ◽  
A New Species

Gorgonian coral specimens from the Holaxonia, families Gorgoniidae and Plexauridae held in the collection of the Santa Barbara Museum of Natural History (SBMNH) were reviewed and evaluated for species identification. The specimens were collected from within, and adjacent areas of, the California Bight. The SBMNH collection has encompassed within it a large percentage of specimens collected by the Allan Hancock Foundation (AHF) ‘Velero’ Expeditions of 1931–1941 and 1948–1985. This historic collection displays an emphasis on species belonging to the Holaxonia, particularly the gorgoniids and plexaurids; thus, this second part presents a thorough discussion of well-known genera from within the California Bight, with more extensive discussions of several genera that have historically, and currently, led to confusion (and thus, misidentification). A brief discussion of a California Bight grouping, referred to within as the “red whips,” is presented; this grouping encompasses several species with very similar colony appearance across a number of genera. Two species, the gorgoniid Leptogorgiachilensis (Verrill, 1868) and the plexaurid Chromoplexauramarki (Kükenthal, 1913) each required the designation of a neotype from within the collection. A new species in the genus Eugorgia Verrill, 1868, a whip or thread-like form belonging to the family Gorgoniidae, is described. One additional plexaurid genus (Placogorgia) is discussed, a genus not commonly reported for the California Bight region. This is the first comprehensive work, in three parts, focusing on all species of gorgonian coral known to inhabit the California Bight. This paper, Part II of the full work, continues the systematic review of all species represented in the Santa Barbara Museum of Natural History research collection begun in Part I.

scholarly journals Genomic sequencing of Phyllosticta citriasiana provide insight into its conservation and diversification with closely related Phyllosticta species associated with citrus

2019 ◽  
Author(s):  
Mingshuang Wang ◽  
Bei Liu ◽  
Ruoxin Ruan ◽  
Yibing Zeng ◽  
Jinshui Luo ◽  
...  
Keyword(s):  
Tan Spot ◽  
Secreted Proteins ◽  
Comparative Genomic ◽  
Orphan Genes ◽  
Core Set ◽  
Genomic Analyses ◽  
Genetic Mechanisms ◽  
Or Gene ◽  
Species Specific ◽  
Insight Into

AbstractPhyllosticta citriasiana is the causal agent of the pomelo tan spot. Here, we presented the ~34Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with other two Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pairwise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. Three Phyllosticta species shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (2040), in complete contrast to that of P. citriasiana (371) and P. citricarpa (262). Most of the orphan genes were functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites (SM) biosynthesis clusters were identified in the three Phyllosticta species, 21 of them are highly conserved among these species while the remaining 2 showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of Phyllosticta species associated with citrus and paves the way to identify effectors that function in infection of citrus plants.

scholarly journals Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

Wallametopa (Amphipoda, Stenothoidae) from South Africa, with description of a new species

Crustaceana ◽  
2016 ◽  
Vol 89 (14) ◽  
pp. 1669-1676
Author(s):  
Michael L. Zettler ◽  
Franziska U. Glück
Keyword(s):  
South Africa ◽  
New Species ◽  
First Record ◽  
Western Cape ◽  
The Family ◽  
A New Species

A new species of the family Stenothoidae,Wallametopa cylindricasp. nov., is described from samples collected in 2015 in the Knysna Estuary, Western Cape, South Africa. This is the first record of the genusWallametopain South Africa, a genus now being represented by two species found in Africa, Madagascar and Australia.Wallametopa cylindricais closely related to the Australian and MadagascanW. cabonBarnard, 1974, from which it differs by having a distinct cylindrical elongation of the merus of gnathopod 1 in both sexes but more striking in males. Both the basis and the merus of gnathopod 2 are also acutely produced postero-distally. The palmar margin of the propodus of gnathopod 2 in males is strongly, irregularly incised and with a deep, broad excavation (larger male). The dactylus reaches the whole length of the propodus and is densely setose on the inner margin.

scholarly journals Marseilleviruses: An Update in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Dehia Sahmi-Bounsiar ◽  
Clara Rolland ◽  
Sarah Aherfi ◽  
Hadjer Boudjemaa ◽  
Anthony Levasseur ◽  
...  
Keyword(s):  
Deep Sea ◽  
Environmental Water ◽  
Comparative Genomic ◽  
Acanthamoeba Polyphaga ◽  
Deep Sea Sediment ◽  
Worldwide Distribution ◽  
The Family ◽  
Genomic Analyses ◽  
Giant Viruses ◽  
Rats And Mice

The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.

scholarly journals A new species of the spider genus Cangoderces (Araneae, Telemidae) from South Africa

2018 ◽  
Vol 59 (1) ◽  
pp. 37-46
Author(s):  
Chunxia Wang ◽  
Shuqiang Li ◽  
Charles R. Haddad
Keyword(s):  
South Africa ◽  
New Species ◽  
Leaf Litter ◽  
The Family ◽  
A New Species

A new species of the spider family Telemidae from South Africa, Cangodercesglobosa sp. n., is diagnosed, described and illustrated. This is the second species of the family to be recorded from the country. Consistent with the habits of most Afrotropical telemids, C.globosa sp. n. was collected by sifting leaf litter in forests.

scholarly journals Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

2021 ◽  
Vol 12 ◽  
Author(s):  
Yisong Li ◽  
Meng Wang ◽  
Zhong-Zhi Sun ◽  
Bin-Bin Xie
Keyword(s):  
Secondary Metabolism ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Genomic Features ◽  
Separate Genus ◽  
The Family ◽  
Genomic Analyses ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Close Relatives

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

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