Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae, isolated from a surface seawater sample

Zhang, Xiaomei; Zhang, Dao‐Feng; Zhang, Yuan-Lan

doi:10.1007/s10482-021-01531-9

Cited by 3 publications

(2 citation statements)

References 36 publications

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“…The current taxonomic framework of the family Erythrobacteraceae was established mainly by using phylogeny based on 288 core genes [ 21 ] and was named ery288 in this study. With ery288 and the substitution model LG + F + R9 for IQ-TREE as the previous report (with manually controlled workflow) [ 21 ], an SM phylogeny with an identical topology was recovered by using EasyCGTree [ 28 ]. Most genera of this family can be recovered as monophyletic groups in the phylogeny of ery288 inferred with FastTree employed by EasyCGTree, except the genera Alteriqipengyuania , Croceibacterium , and Qipengyuania [ 27 ].…”

Section: Resultsmentioning

confidence: 99%

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

Zhang,

He,

Shao

et al. 2023

BMC Bioinformatics

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Background Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. Results EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines. Conclusions EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4).

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Section: Resultsmentioning

confidence: 99%

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

Zhang,

He,

Shao

et al. 2023

BMC Bioinformatics

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“…This genus is characterized by yellow-coloured colonies on agar plates, the lack of bacteriochlorophyll a, the presence of summed feature 8 (C 18 : 1 ω7c and/or C 18 : 1 ω6c) as the major fatty acid, diphosphatidylglycerol and phosphatidylethanolamine as the major polar lipids, ubiquinone 10 as the major respiratory quinone, genomic DNA G+C contents ranging from 60.5 to 67.0%, and a mesophilic temperature range for optimal growth [1]. Bacteria of this genus have often been isolated from marine environments, such as tidal flat [3], mangrove sediments [4,5], seawater [6] and sea urchin [7]. Some strains have been isolated from terrestrial environments, such as contaminated air [8], lake sediment [9], wetland freshwater [10] and desert soil [11].…”

Section: Introductionmentioning

confidence: 99%

Tsuneonella litorea sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment

Liu

Pei

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, non-motile and pleomorphic bacterium designated as YG55T was isolated from a coastal sediment sample. Growth was found to occur at 10–37 °C (optimum, 28 °C), at pH 6–9 (optimum, pH 8) and in 0–6 % NaCl (optimum, 1 %). The results of 16S rRNA gene-based analysis showed that strain YG55T was related to the members of the genus Tsuneonella and shared the highest identity of 99.4 % with Tsuneonella dongtanensis GDMCC 1.2307T, followed by Tsuneonella troitsensis JCM 17037T (98.4 %). The phylogenomic results indicated that strain YG55T formed an independent branch distinct from the reference type strains. The 22.7 and 21.8 % digital DNA–DNA hybridization (dDDH) values and 83.0 and 81.8 % average nucleotide identity (ANI) values between strain YG55T and the two relatives were below the species definition thresholds of 70 % (dDDH) and 95–96 % (ANI), indicating that the strain represents a novel genospecies. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain YG55T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C14 : 0 2OH and C16 : 0; the main polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; the respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.03 Mbp and 66.98 %. The strain contained carotenoid biosynthesis genes and could produce carotenoids. Based on its genotypic and phenotypic characteristics, strain YG55T is concluded to represent a novel species of the genus Tsuneonella , for which the name Tsuneonella litorea sp. nov. is proposed. The type strain is YG55T (=GDMCC 1.2590 T=KCTC 82812T).

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Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment

Liu,

Pei,

et al. 2024

Curr Microbiol

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Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae, isolated from a surface seawater sample

Cited by 3 publications

References 36 publications

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

Tsuneonella litorea sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment

Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment

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