scholarly journals Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6366 ◽  
Author(s):  
Han Ming Gan ◽  
Melvin V.L. Lee ◽  
Michael A. Savka
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Comparative Genomics ◽  
Type Strain ◽  
Single Species ◽  
Agrobacterium Radiobacter ◽  
Tree Construction ◽  
Large Genome Size ◽  
Genome Scale ◽  
Genome Accession ◽  
First Time

The reportedAgrobacterium radiobacterDSM 30174Tgenome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced theAgrobacterium radiobactertype strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome ofAgrobacterium tumefaciensB6T, enabling for the first time, a proper comparative genomics of these contentiousAgrobacteriumspecies. We provide concrete evidence that the previously reportedAgrobacterium radiobactertype strain genome (Accession Number:ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose thatAgrobacterium tumefaciensbe reclassified asAgrobacterium radiobactersubsp.tumefaciensand thatAgrobacterium radiobacterretains it species status with the proposed name ofAgrobacterium radiobactersubsp.radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of bothAgrobacterium radiobacterandAgrobacterium tumefaciensinto a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates thatAgrobacterium radiobacterNCPPB3001 is sufficiently divergent fromAgrobacterium tumefaciensto propose two independent sub-clades. Third,Agrobacterium tumefaciensdemonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively thanAgrobacterium radiobacter.

scholarly journals Strain ATCC 4720T is the authentic type strain of Agrobacterium tumefaciens, which is not a later heterotypic synonym of Agrobacterium radiobacter

2020 ◽  
Vol 70 (9) ◽  
pp. 5172-5176 ◽  
Author(s):  
Encarna Velázquez ◽  
José David Flores-Félix ◽  
Fernando Sánchez-Juanes ◽  
José M. Igual ◽  
Álvaro Peix
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Type Strain ◽  
Type Species ◽  
Strain Atcc ◽  
Agrobacterium Radiobacter ◽  
Culture Collections ◽  
Content Type ◽  
Link Type ◽  
Eighth Edition ◽  
Original Type

The original type strains of Agrobacterium radiobacter and Agrobacterium tumefaciens recorded in the eighth edition of Bergey’s Manual of Determinative Bacteriology published in 1974 were NCIB 9042T and ATCC 4720T, respectively. However, in the list of the valid names of bacteria compiled in 1980, both strains were changed, A. radiobacter NCIB 9042T to ATCC 19358T and A. tumefaciens ATCC 4720T to ATCC 23308T. These changes were unjustified, particularly in the case of A. tumefaciens whose type strain was replaced by another strain from the same collection, although the original type strain ATCC 4720T was never lost and it is currently available in several culture collections. Therefore, we request that the type strain of A. tumefaciens be corrected from ATCC 23308T to ATCC 4720T.

scholarly journals Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Can Yuan ◽  
Xiufen Sha ◽  
Miao Xiong ◽  
Wenjuan Zhong ◽  
Yu Wei ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Species Discrimination ◽  
Chloroplast Genomes ◽  
Genomic Arrangement ◽  
Phylogenetic Implications ◽  
Solid Foundation ◽  
Conserved Gene ◽  
Fine Resolution ◽  
Genome Scale ◽  
First Time

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

scholarly journals Remarkable Species Diversity of the Leafhopper Genus Xestocephalus (Hemiptera: Cicadellidae: Aphrodinae) in Thailand

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 514
Author(s):  
Zonglei Liang ◽  
Christopher H. Dietrich ◽  
Wu Dai
Keyword(s):  
New Species ◽  
Species Diversity ◽  
Single Species ◽  
Comparative Morphology ◽  
Malaise Trap ◽  
Field Sampling ◽  
Tropical Regions ◽  
Trap Field ◽  
The World ◽  
First Time

Xestocephalus Van Duzee is among the most common and widespread genera of Cicadellidae in the temperate and tropical regions of the world. In the present study, 205 specimens of the genus Xestocephalus were collected in Thailand, whereas only a single species of the genus was recorded previously using Malaise trap field sampling, studied by comparative morphology. Seventeen species were recognized, including twelve new species: X. binarius sp. nov., X. chrysanthemum sp. nov., X. cowboyocreus sp. nov., X. densprint sp. nov., X. dimiprocessus sp. nov., X. exproiecturus sp. nov., X. gracilus sp. nov., X. limpidissimus sp. nov., X. malleus sp. nov., X. nonattribus sp. nov., X. recipinams sp. nov., and X. tenusis Liang sp. nov. Four species were recorded in Thailand for the first time: Xestocephalus abyssinicus Heller and Linnavuori, Xestocephalus asper Linnavuori, Xestocephalus ishidae Matsumura, and Xestocephalus toroensis Matsumura. Detailed morphological descriptions of all 17 species are given; photographs of external habitus and male genitalia of the species from Thailand are provided. A checklist of species of the genus is also given, and a key to all Thailand Xestocephalus species is also provided.

scholarly journals A Synopsis of Orthotrichum s. lato (Bryophyta, Orthotrichaceae) in China, with Distribution Maps and a Key to Determination

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 499
Author(s):  
Vítězslav Plášek ◽  
Zuzana Komínková ◽  
Ryszard Ochyra ◽  
Lucie Fialová ◽  
Shuiliang Guo ◽  
...  
Keyword(s):  
Single Species ◽  
Herbarium Specimens ◽  
Distribution Maps ◽  
First Time

A total of 46 species and two varieties of the traditionally interpreted genus Orthotrichum are currently known to occur in China. They represent five genera, including Orthotrichum (29 species), Lewinskya (14 species and two varieties), and Nyholmiella and Leratia that are represented by a single species each. The fifth genus Florschuetziella, also consisting of only one species, F. scaberrima, is an entirely neglected representative of the China’s moss flora. A list of all accepted taxa is presented and for each taxon all literature records and herbarium specimens are enumerated for provinces in which they have been recorded, and their distribution is mapped. A key to determination of Chinese orthotrichalean mosses is presented. A chronological list of 63 species and varieties and two designations, O. catagonioides and O. microsporum which have never been validly published, reported from China in the years 1892–2020 is presented. Four species, Orthotrichum brasii, O. hooglandii, O. elegans and O. gymnostomum are excluded from the bryoflora of China and Lewinskya affinis var. bohemica and Orthotrichum schimperi are recorded for the first time from this country. Phytogeography of the Chinese taxa of the orthotrichalean mosses is considered and they are grouped into eight phytogeographical elements and five sub-elements.

First record of the genus Yalvaciana (Tettigoniidae; Tettigoniinae; Platycleidini) with the description of a new species from India

Zootaxa ◽  
2021 ◽  
Vol 4966 (5) ◽  
pp. 591-595
Author(s):  
MUZAMIL SYED SHAH ◽  
MOHD KAMIL USMANI
Keyword(s):  
New Species ◽  
Single Species ◽  
First Record ◽  
Key To Species ◽  
First Time ◽  
A New Species ◽  
Zoology Department

The genus Yalvaciana Ciplak et.al (2002) is reported for the first time from India represented by a new species. Previously the genus comprised a single species, Yalvaciana yalvaci Demirsoy, (1974). Brief information about morphology, distribution and key to species are given. The Holotype has been deposited in the Museum of Zoology Department, AMU (ZDAMU). 

scholarly journals Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

2021 ◽  
Author(s):  
Donovan H Parks ◽  
Maria Chuvochina ◽  
Peter R Reeves ◽  
Scott A Beatson ◽  
Philip Hugenholtz
Keyword(s):  
Escherichia Coli ◽  
Type Strain ◽  
Shigella Flexneri ◽  
Laboratory Strain ◽  
Single Species ◽  
Species Definition ◽  
E Coli ◽  
Shigella Species ◽  
K 12 ◽  
Common Laboratory

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to 'E. flexneri') because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli. Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli, present evidence supporting this reclassification, and show that assigning E. coli/Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.

scholarly journals NEUROPTERA OF THE AMAZON BASIN Part 9. Albardiinae

1983 ◽  
Vol 13 (3-4) ◽  
pp. 697-699 ◽  
Author(s):  
Norman D. Penny ◽  
Keyword(s):  
Amazon Basin ◽  
Single Species ◽  
First Time

Summary The Albardiinae Weele, 1908 (Neuroptera: Ascalaphidae) with a single species, Albardia furcata, is recorded for the first time from the Amazon Basin.

NEW LOCI IN DICTYOSTELIUM DISCOIDEUM DETERMINING PIGMENT FORMATION AND GROWTH ON BACILLUS SUBTILIS

Genetics ◽  
1980 ◽  
Vol 96 (1) ◽  
pp. 115-123
Author(s):  
James H Morrissey ◽  
Steven Wheeler ◽  
William F Loomis
Keyword(s):  
Bacillus Subtilis ◽  
Dictyostelium Discoideum ◽  
Type Strain ◽  
Wild Type Strain ◽  
Wild Type ◽  
Linkage Groups ◽  
New Mutation ◽  
Pigment Formation ◽  
Complementation Groups ◽  
First Time

ABSTRACT Seventeen independently isolated pigmentless (white) mutations in Dictyostelium discoideum are all recessive and fall into three complementation groups identifying two new whi loci in addition to the previously characterized whiA locus. whiB and whiC map to linkage groups III and IV, respectively. In addition, it was discovered that our laboratory stock of NC4, the wild-type strain from which these mutants were derived, has spontaneously lost the ability to grow on Bacillus subtilis. This new mutation, bsgB500, maps to linkage group VII and is not allelic to bsgA. bsgB500 is the first spontaneously derived mutation in D. discoideum that can be used to select heterozygous diploids, and for the first time allows genetic analysis to be routinely performed on strains derived from an unmutagenized background.

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