Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cultivation Procedure and DNA Extraction
2.2. Genome Sequencing and Assembly
2.3. Selection of Reference Genomes and Phylogenomic Analysis
2.4. Core- and Pan-Genome Analysis
2.5. Analysis of Functional Genes
3. Results
3.1. Genome Characteristics of Mc. heyeri H2T
3.2. Genome-Based Phylogeny
3.3. Pan-Genome Analysis
3.4. MMO-Encoding Genes
3.5. Nitrogenase-Encoding Genes
3.6. Genomic Determinants of Flagella-Based Motility
3.7. Phototrophy-Related Genes
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Group | Organism | Genome Assembly | Size (MB) | Contigs | G+C Content (mol %) | Proteins | rRNAs (5S, 16S, 23S) | tRNAs | pMMO1 | pMMO2 | sMMO | pXMO |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Methylocystis | Mc. heyeri H2T | GCA_004802635.2 | 4.55 | 1 | 63.1 | 3976 | 3, 3, 3 | 53 | 2 | 1 | 1 | none |
Mc. bryophila S285 | GCA_002117405.1 | 4.53 | 1 | 63.2 | 4148 | 2, 2, 2 | 47 | 2 | 1 | 1 | 1 | |
Mc. sp. SC2 | GCA_000304315.1 | 3.77 | 1 | 63.4 | 3545 | 1,1,1 | 46 | 2 | 1 | none | none | |
Mc. sp. ATCC 49242 | GCA_000188155.3 | 4.73 | 7 | 62.8 | 4285 | 2,2,2 | 53 | 2 | none | none | none | |
Mc. sp. B8 | GCA_005771425.1 | 3.41 | 28 | 61.2 | 3153 | 1, 1, 1 | 47 | 1 | 1 | none | none | |
Mc. sp. SB2 | GCA_000499825.2 | 3.64 | 158 | 62.7 | 3392 | 1, 1, 1 | 45 | 2 | none | none | 1 | |
Mc. rosea SV97T | GCA_000372845.1 | 3.91 | 4 | 62.5 | 3639 | 1,1,1 | 48 | 2 | none | none | 1 | |
Mc. rosea GW6 | GCA_003855495.1 | 3.64 | 1 | 62.8 | 3441 | 1,1,1 | 48 | 2 | none | none | 1 | |
Mc. rosea BRCS1 | GCA_009685175.1 | 3.80 | 3 | 62.7 | 3499 | 1, 1, 1 | 49 | 2 | none | none | 1 | |
Mc. parvus BRCS2 | GCA_009685195.1 | 4.53 | 1 | 63.4 | 4185 | 2,2,2 | 48 | 2 | 1 | none | none | |
Mc. parvus OBBPT | GCA_000283235.1 | 4.48 | 108 | 63.4 | 4128 | 1, 1, 1 | 46 | 1 | 1 | none | none | |
Mc. hirsuta CSC1T | GCA_003722355.1 | 4.21 | 4 | 62.4 | 4036 | 1, 1, 1 | 49 | 2 | none | 1 | 1 | |
Mc. sp. MitZ-2018 | GCA_003113245.1 | 4.36 | 55 | 62.5 | 3962 | 1, 1, 1 | 50 | 2 | none | none | 1 | |
Methylosinus | Ms. sporium SM89A | GCA_007004125.1 | 4.59 | 161 | 64.5 | 4155 | 1, 1, 1 | 46 | 1 | 1 | 2 | none |
Ms. sporium DSM 17706T | GCA_003113265.1 | 3.8 | 55 | 65.2 | 3506 | 1, 1, 1 | 41 | 1 | 1 | 2 | none | |
Ms trichosporium OB3bT | GCA_002752655.1 | 4.5 | 1 | 65.8 | 4546 | 3, 3, 3 | 53 | 2 | none | 1 | none | |
Ms. sp. 3S-1 | GCA_001675455.1 | 4.76 | 159 | 66.0 | 4209 | 1, 1, 1 | 48 | 1 | none | 1 | none | |
Ms. sp. PW1 | GCA_000745215.1 | 5.13 | 12 | 64.7 | 4657 | 4, 4, 5 | 58 | 2 | 1 | 1 | none | |
Ms. sp. LW3 | GCA_000527115.1 | 5.09 | 6 | 64.7 | 4502 | 3,3,3 | 52 | 2 | 1 | 1 | none | |
Ms. sp. LW4 | GCA_000379125.1 | 4.82 | 16 | 64.9 | 4452 | 3,3,3 | 53 | 2 | 1 | 1 | none | |
Ms. sp. R-45379 | GCA_001644125.1 | 4.97 | 319 | 64.4 | 4446 | 1, 1, 1 | 46 | 1 | 1 | 1 | 1 | |
Ms. sp. Ce-a6 | GCA_009811655.1 | 4.09 | 119 | 65.4 | 3724 | 1, 1, 1 | 51 | 1 | 1 | none | none | |
Ms. sp. C49 | GCA_009936375.1 | 4.71 | 1 | 64.9 | 4317 | 3, 3, 3 | 52 | 2 | 1 | 1 | none |
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Oshkin, I.Y.; Miroshnikov, K.K.; Grouzdev, D.S.; Dedysh, S.N. Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms 2020, 8, 768. https://doi.org/10.3390/microorganisms8050768
Oshkin IY, Miroshnikov KK, Grouzdev DS, Dedysh SN. Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms. 2020; 8(5):768. https://doi.org/10.3390/microorganisms8050768
Chicago/Turabian StyleOshkin, Igor Y., Kirill K. Miroshnikov, Denis S. Grouzdev, and Svetlana N. Dedysh. 2020. "Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus" Microorganisms 8, no. 5: 768. https://doi.org/10.3390/microorganisms8050768