Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms
Abstract
:1. Introduction
2. Materials and Methods
2.1. RNA Virus Detection by PCR
2.2. DNA Virus Detection by PCR
2.3. Sequencing of PCR Products
2.4. Phylogenetic Analysis
2.5. Pairwise Sequence Identity Comparisons
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Accession Number | Sequence | Accession Number | Sequence |
---|---|---|---|
LC534420 | 2011_Aug_Sd-a | LC534488 | 2013_Jul_3715 |
LC534421 | 2011_Aug_Sd-b | LC534489 | 2013_Aug_3715 |
LC534422 | 2011_Aug_Sd-c | LC534490 | 2013_Sep_3715 |
LC534423 | 2011_Aug_Sd-d | LC534491 | 2013_Oct_3715 |
LC534424 | 2011_Dec_Sd-a | LC534492 | 2014_Jan_3714 |
LC534425 | 2011_Dec_Sd-b | LC534493 | 2014_Jan_3715 |
LC534426 | 2011_Dec_Sd-c | LC534494 | 2014_Apr_3714 |
LC534427 | 2011_Dec_Sd-d | LC534495 | 2014_May_3714 |
LC534428 | 2011_Dec_Sd-e | LC534496 | 2014_Jun_3714 |
LC534429 | 2011_Jul_Sd-a | LC534497 | 2014_Jun_3715 |
LC534430 | 2011_Jul_Sd-d | LC534498 | 2014_Jul_3715 |
LC534431 | 2011_Jul_Sd-e | LC534499 | 2014_Aug_3715 |
LC534432 | 2011_Jul_Sd-f | LC534500 | 2014_Sep_3715 |
LC534433 | 2011_Nov_Sd-a | LC534501 | 2014_Oct_3715 |
LC534434 | 2011_Nov_Sd-b | LC534502 | 2014_Nov_3715 |
LC534435 | 2011_Oct_Sd-a | LC534503 | 2011_Jul_3712 |
LC534436 | 2011_Oct_Sd-b | LC534504 | 2011_Nov_3712 |
LC534437 | 2011_Oct_Sd-c | LC534505 | 2011_Dec_3712-A |
LC534438 | 2011_Sep_Sd-a | LC534506 | 2011_Dec_3712-B |
LC534439 | 2011_Sep_Sd-b | LC534507 | 2013_May_3712 |
LC534440 | 2013_Aug_Sd | LC534508 | 2014_Feb_3712-A |
LC534441 | 2013_Dec_Sd-a | LC534509 | 2014_Feb_3712-B |
LC534442 | 2013_Dec_Sd-b | LC534510 | 2014_Apr_3712 |
LC534443 | 2013_Dec_Sd-c | LC534511 | 2014_Jun_3712 |
LC534444 | 2013_Dec_Sd-d | LC534512 | 2014_Jul_3712 |
LC534445 | 2013_Dec_Sd-e | LC534513 | 2014_Sep_3712 |
LC534446 | 2013_Dec_Sd-f | LC534514 | 2014_Oct_3712 |
LC534447 | 2013_Jul_Sd | LC534515 | 2014_Nov_3712 |
LC534448 | 2013_Jun_Sd-a | LC534516 | 2015_Jan_3712 |
LC534449 | 2013_Jun_Sd-b | LC534517 | 2015_Feb_3712-A |
LC534450 | 2013_May_Sd-a | LC534518 | 2015_Feb_3712-B |
LC534451 | 2013_May_Sd-b | LC534519 | 2015_Mar_3712-A |
LC534452 | 2013_Nov_Sd-a | LC534520 | 2015_Mar_3712-B |
LC534453 | 2013_Nov_Sd-b | LC534521 | 2014_Jan_Sd |
LC534454 | 2013_Nov_Sd-c | LC534522 | 2014_Feb_Sd |
LC534455 | 2013_Nov_Sd-d | LC534523 | 2014_May_Sd |
LC534456 | 2013_Oct_Sd | LC534524 | 2011_Sep_3715 |
LC534457 | 2014_Apr_Sd | LC534525 | 2011_Sep_3714 |
LC534458 | 2014_Feb_Sd-a | LC534526 | 2011_Aug_3714 |
LC534459 | 2014_Feb_Sd-b | LC534527 | 2011_Jul_3714 |
LC534460 | 2014_Feb_Sd-d | LC534528 | 2015_Mar_3715 |
LC534461 | 2014_Feb_Sd-e | LC534529 | 2015_Feb_3714 |
LC534462 | 2014_Feb_Sd-g | LC534530 | 2014_Mar_3714 |
LC534463 | 2014_Feb_Sd-h | LC534531 | 2014_Mar_3715 |
LC534464 | 2014_Feb_Sd-i | LC534532 | 2014_Feb_3714-a |
LC534465 | 2014_Feb_Sd-j | LC534533 | 2014_Feb_3714-b |
LC534466 | 2014_Jan_Sd-a | LC534534 | 2014_Feb_3715 |
LC534467 | 2014_Jan_Sd-b | LC534535 | 2011_Dec_3714 |
LC534468 | 2014_Jun_Sd | LC534536 | 2013_May_3714 |
LC534469 | 2014_May_Sd-a | LC534537 | 2013_May_3715 |
LC534470 | 2014_May_Sd-b | LC534538 | 2013_Jun_3714 |
LC534471 | 2014_Nov_Sd-a | LC534539 | 2011_Aug_3715 |
LC534472 | 2014_Nov_Sd-c | LC534540 | 2013_Sep_3714 |
LC534473 | 2014_Nov_Sd-d | LC534541 | 2013_Oct_3714 |
LC534474 | 2014_Nov_Sd-e | LC534542 | 2013_Nov_3715 |
LC534475 | 2015_Jan_Sd | LC534543 | 2013_Dec_3715 |
LC534476 | 2015_Mar_Sd-a | LC534544 | 2013_Nov_3714 |
LC534477 | 2015_Mar_Sd-b | LC534545 | 2014_Apr_3715 |
LC534478 | 2011_Jul_3714 | LC534546 | 2014_Jun_3714 |
LC534479 | 2011_Jul_3715 | LC534547 | 2014_Jun_3715 |
LC534480 | 2011_Aug_3715 | LC534548 | 2014_Aug_3714 |
LC534481 | 2011_Sep_3715 | LC534549 | 2014_Nov_3714 |
LC534482 | 2011_Oct_3715 | LC534550 | 2014_Oct_3715 |
LC534483 | 2011_Nov_3714 | LC534551 | 2014_Oct_3714 |
LC534484 | 2011_Nov_3715 | LC534552 | 2014_Sep_3714 |
LC534485 | 2011_Dec_3715 | LC534553 | 2014_Nov_3715 |
LC534486 | 2013_Jun_3715 | LC534554 | 2015_Jan_3714 |
LC534487 | 2013_Jul_3714 | LC534555 | 2015_Jan_3715 |
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Date | ssRNA Virus, Mplsc2F/R* | ssDNA Virus, BDVrepF1/R1** | |||||||
---|---|---|---|---|---|---|---|---|---|
Sediment Pore Water | C. setoensis | C. tenuissimus | Sediment Pore Water | C. setoensis | C. tenuissimus | ||||
NIES-3712 | NIES-3714 | NIES-3715 | NIES-3712 | NIES-3714 | NIES-3715 | ||||
2011 | Jul 23 | A, E, I, K | E | E | E | - | - | T | - |
2011 | Aug 10 | A, I, J, R | - | - | E | - | - | T | T |
2011 | Sep 7 | C, N | - | - | E | - | - | T | T |
2011 | Oct 3 | A, C, J | - | - | E | - | - | - | - |
2011 | Nov 4 | C, D | D | D | E | - | - | - | - |
2011 | Dec 12 | A, C, D, E, Q | C, D | - | E | - | - | T | - |
2013 | May 21 | A, O | A | - | - | - | - | T | T |
2013 | Jun 28 | J, R | - | - | E | - | - | T | - |
2013 | Jul 10 | A | - | E | E | - | - | - | - |
2013 | Aug 7 | J | - | - | E | - | - | - | - |
2013 | Sep 5 | - | - | - | E | - | - | V | - |
2013 | Oct 18 | S | - | - | E | - | - | V | - |
2013 | Nov 20 | A, B, G, J | - | - | - | - | - | V | T |
2013 | Dec 19 | A, B, C, L, N, Q | - | - | - | - | - | - | T |
2014 | Jan 22 | A, C, | - | N | Q | U | - | - | - |
2014 | Feb 19 | A, C, G, J, L, N, Q, S | F, H | - | - | U | - | T, V | T |
2014 | Mar 12 | - | - | - | - | - | - | T | T |
2014 | Apr 17 | A | C | A | - | - | - | - | T |
2014 | May 22 | A, R | - | A | - | U | - | - | - |
2014 | Jun 16 | A | A | C | A | - | - | T | T |
2014 | Jul 14 | - | A | - | E | - | - | - | - |
2014 | Aug 11 | - | - | - | E | - | - | T | - |
2014 | Sep 17 | - | B | - | E | - | - | T | - |
2014 | Oct 15 | - | C | - | E | - | - | T | T |
2014 | Nov 12 | A, C, G, K | C | - | E | - | - | T | T |
2015 | Jan 21 | C | C | - | - | - | - | T | T |
2015 | Feb 24 | - | C, P | - | - | - | - | T | - |
2015 | Mar 25 | M, N | C, O | - | - | - | - | - | T |
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Tomaru, Y.; Kimura, K. Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms. Diversity 2020, 12, 225. https://doi.org/10.3390/d12060225
Tomaru Y, Kimura K. Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms. Diversity. 2020; 12(6):225. https://doi.org/10.3390/d12060225
Chicago/Turabian StyleTomaru, Yuji, and Kei Kimura. 2020. "Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms" Diversity 12, no. 6: 225. https://doi.org/10.3390/d12060225
APA StyleTomaru, Y., & Kimura, K. (2020). Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms. Diversity, 12(6), 225. https://doi.org/10.3390/d12060225