Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Bowman, John P.

doi:10.1099/ijsem.0.005991

Cited by 4 publications

(3 citation statements)

References 82 publications

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“…Our arbitrary Candidatus names have begun to be cited in research publications [7][8][9][10][11][12], but, curiously, the names cannot be validly published under the SeqCode, as the SeqCode rules explicitly exclude use of arbitrary components in the creation of names, despite over a century and a half of precedents for such practice [13] and recent adoption of arbitrary arti cial su xes in the quest to replace descriptive names for prokaryotic phyla and kingdoms with those built from type genera [14,15]. If the SeqCode community prefers not to use our arbitrary names, they should at least rise to the challenge of creating tens of thousands of new names that do meet their own arbitrary rules.…”

Section: Discussionmentioning

confidence: 99%

Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214

Pallen

2024

Preprint

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Here, an established approach to the generation of well-formed arbitrary Latinate names at a scale has been adopted and adapted to name tens of thousands of new, but unnamed taxa within GTDB Release r214.1. New Latinate Candidatus names have been created and assigned to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species. New Candidatus names for bacterial phyla include Ca. Afuciota, Ca.Axiviota, Ca. Bobupiota, Ca. Fitepiota, Ca. Hubebiota, Ca.Ibociota, Ca. Inuciota, Ca. Luxamiota, Ca. Megaciota, Ca.Nasexiota, Ca. Oviciota, Ca. Ucifiota, and Ca. Uvuciota, while new names for archaeal phyla include Ca. Acigarchota and Ca.Omefarchota. These efforts show that the creation of arbitrary names for prokaryotic taxa remains sustainable, despite the relentless progress of discovery.

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Section: Discussionmentioning

confidence: 99%

Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214

Pallen

2024

Preprint

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“…Draper v1.0 were downloaded from https://www.vaccinium.org/genomes (accessed on 20 September 2023). Novel genes were annotated in the following databases: NR (NCBI non-redundant protein sequences), NT (NCBI non-redundant nucleotide sequences), Pfam (Protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (a manually annotated and reviewed protein sequence database), KO (KEGG Ortholog database), and GO (pannzer2 database) [48,49]. TFs were predicted using the plantTF database from https://planttfdb.gao-lab.org (accessed on 15 December 2023) and online software Plant-PAN 4.0 [50,51].…”

Section: Gene Functional Annotationmentioning

confidence: 99%

Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry (Vaccinium spp.) Fruit

Tian,

Liu,

Chen

et al. 2024

IJMS

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As a highly economic berry fruit crop, blueberry is enjoyed by most people and has various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids. To obtain more accurate and comprehensive transcripts, the full-length transcriptome of half-highbush blueberry (Vaccinium corymbosum/angustifolium cultivar Northland) obtained using single molecule real-time and next-generation sequencing technologies was reported for the first time. Overall, 147,569 consensus transcripts (average length, 2738 bp; N50, 3176 bp) were obtained. After quality control steps, 63,425 high-quality isoforms were obtained and 5030 novel genes, 3002 long non-coding RNAs, 3946 transcription factor genes (TFs), 30,540 alternative splicing events, and 2285 fusion gene pairs were identified. To better explore the molecular mechanism of flavonoid biosynthesis in mature blueberry fruit, an integrative analysis of the metabolome and transcriptome was performed on the exocarp, sarcocarp, and seed. A relatively complete biosynthesis pathway map of phenylpropanoids, flavonoids, and proanthocyanins in blueberry was constructed. The results of the joint analysis showed that the 228 functional genes and 42 TFs regulated 78 differentially expressed metabolites within the biosynthesis pathway of phenylpropanoids/flavonoids. O2PLS analysis results showed that the key metabolites differentially accumulated in blueberry fruit tissues were albireodelphin, delphinidin 3,5-diglucoside, delphinidin 3-O-rutinoside, and delphinidin 3-O-sophoroside, and 10 structural genes (4 Vc4CLs, 3 VcBZ1s, 1 VcUGT75C1, 1 VcAT, and 1 VcUGAT), 4 transporter genes (1 VcGSTF and 3 VcMATEs), and 10 TFs (1 VcMYB, 2 VcbHLHs, 4 VcWD40s, and 3 VcNACs) exhibited strong correlations with 4 delphinidin glycosides. These findings provide insights into the molecular mechanisms of flavonoid biosynthesis and accumulation in blueberry fruit.

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“…Recently, Bowman reclassified the species of Massilia based on genome-wide and constrained ordination-based analyses of Enzyme commission code data, transferring 35 species from the genus Massilia to the genus Telluria . Members of the genus Massilia are characterized as aerobic, Gram-stain-negative, motile, non-spore-forming rods [8]. The genus Agrococcus is a member of the family Microbacteriaceae .…”

Section: Introductionmentioning

confidence: 99%

Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash

Gu,

Hao,

Sun

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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The baijiu fermentation environment hosts a variety of micro-organisms, some of which still remain uncultured and uncharacterized. In this study, the isolation, cultivation and characterization of three novel aerobic bacterial strains are described. The cells of strain REN20T were Gram-negative, strictly aerobic, motile and grew at 26–37 °C, at pH 6.0–9.0 and in the presence of 0–5.0 % (w/v) NaCl. The cells of strain REN29T were Gram-negative, strictly aerobic, motile and grew at 15–30 °C, at pH 6.0–9.0 and in the presence of 0–10.0 % (w/v) NaCl. The cells of strain REN33T were Gram-positive, strictly aerobic, motile and grew at 15–37 °C, at pH 5.0–10.0 and in the presence of 0–7.0 % (w/v) NaCl. The digital DNA–DNA hybridization and average nucleotide identity by orthology values between type strains in related genera and REN20T (20.3–36.8 % and 79.8–89.9 %), REN29T (20.3–36.8 % and 74.5–88.5 %) and REN33T (22.6–48.6 % and 75.8–84.2 %) were below the standard cut-off criteria for the delineation of bacterial species, respectively. Based on polyphasic taxonomy analysis, we propose three new species, Bosea beijingensis sp. nov. (=REN20T=GDMCC 1.2894T=JCM 35118T), Telluria beijingensis sp. nov. (=REN29T=GDMCC 1.2896T=JCM 35119T) and Agrococcus beijingensis sp. nov. (=REN33T=GDMCC 1.2898T=JCM 35164T), which were recovered during cultivation and isolation from baijiu mash.

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Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Abstract: Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species … Show more

Cited by 4 publications

References 82 publications

Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214

Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214

Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry (Vaccinium spp.) Fruit

Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash

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