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Probes for Micromonas

Probes for Micromonas.  Application of the probe MICRO01on natural samples from Roscoff have demonstrated a strong domination of this genus in the picoeukaryotic community

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Probes for Micromonas

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  1. Probes for Micromonas

  2.  Application of the probe MICRO01on natural samples from Roscoff have demonstrated a strong domination of this genus in the picoeukaryotic community  Clones libraries and 18S rDNA sequence analyses from PICODIV have shown the distinction of three clade within the genus Micromonas

  3. RA010516-49 RA010516-55 BL001221-28 RA010613-91 RA010412-45 RA000412-35 RA010412-11 RA000412-127 RA000412-74 RA001219-41 RA000412-81 RA000412-102 RA010516-29 RA001219-33 RA010613-5 RA000609-34 RA000412-89 RA010412-43 RA010516-48 RD010517-1 RA000412-83 Bathycoccus prasinos ALMO2 RA000412-56 Bathycoccus prasinos RCC436 RA010412-15 RA000412-117 BL010320-30 RA001219-63 RA000412-100 RD010517-69 RA000609-15 RD010517-5 Ostreococcus sp. MBIC10636 RD010517-44 RD010517-3 Ostreococcus sp. RCC356 RA010613-50 RA010516-18 RA010412-39 RA000609-36 RA000412-85 Ostreococcus sp. RCC344 RA010516-2 RA010516-12 RD010517-14 RA010516-20 RA000412-115 BL000921-14 Ostreococcus sp. RCC393 Ostreococcus sp. RCC143 86/89 Ostreococcus tauri RA000412-150 Ostreococcus sp. RCC501 Micromonas pusilla CCMP489 RA010412-38 NA11-1 RA010412-10 RA000412-97 RA001219-25 RA010516-21 RA010516-47 NA37-1 Bathycoccus RA010412-92 77/68 RA000412-152 RA010613-119 RA010516-39 + ME1-3 RA000412-157 RA010516-36 RA000907-56 BL000921-10 100/100 BL001221-10 ANT37-4 BL001221-4 RA000412-153 BL010320-1 Micromonas sp. RCC434 RA010516-35 RA000412-37 RA000907-63 100/99 83/80 A -/61 Ostreococcus + ME1-1 92/95 0.1 88/98 100/99 B C D 98/94 A Micromonas 100/100 -/- -/- -/- B -/- -/- 81/75 100/100 RA000907-39 RA000907-9 RA010613-139 -/- RA000412-36 Micromonas pusilla CCMP490 C RD010517-66 RA010412-7 -/- ANT37-3 Mantoniella Mantoniella squamata Mantoniella antarctica RCC391 Mamiella sp. Dolichomastix lepitoda 98/93 Crustomastix sp. MBIC10709 Tree from Laure paper

  4.  Application of the probe MICRO01on natural samples from Roscoff have demonstrated a strong domination of this genus in the picoeukaryotic community  Clones libraries and 18S rDNA sequence analyses from PICODIV have shown the distinction of three clade within the genus Micromonas Design probe for each of the three clade

  5. Probe Design Total and partial sequences of Mamiellales clade from the PICODIV database were aligned with clustalW and check manualy using phylowin software. After re-alignment, a tree were constructed with seaview software in order to validate the disctinction of the three clades observed in the tree from ARB software  Probe design and probe match function of ARB were used on selected sequences from each of the three clade of micromonas.

  6. 86/89 Bathycoccus 77/68 + ME1-3 100/100 100/99 83/80 A -/61 Ostreococcus RA010516-49 RA010516-55 BL001221-28 RA010613-91 RA010412-45 RA000412-35 RA010412-11 RA000412-127 RA000412-74 RA001219-41 RA000412-81 RA000412-102 RA010516-29 RA001219-33 RA010613-5 RA000609-34 RA000412-89 RA010412-43 RA010516-48 RD010517-1 RA000412-83 Bathycoccus prasinos ALMO2 RA000412-56 Bathycoccus prasinos RCC436 RA010412-15 RA000412-117 BL010320-30 RA001219-63 RA000412-100 RD010517-69 RA000609-15 RD010517-5 Ostreococcus sp. MBIC10636 RD010517-44 RD010517-3 Ostreococcus sp. RCC356 RA010613-50 RA010516-18 RA010412-39 RA000609-36 RA000412-85 Ostreococcus sp. RCC344 RA010516-2 RA010516-12 RD010517-14 RA010516-20 RA000412-115 BL000921-14 Ostreococcus sp. RCC393 Ostreococcus sp. RCC143 Ostreococcus tauri RA000412-150 Ostreococcus sp. RCC501 Micromonas pusilla CCMP489 RA010412-38 NA11-1 RA010412-10 RA000412-97 RA001219-25 RA010516-21 RA010516-47 NA37-1 RA010412-92 RA000412-152 RA010613-119 RA010516-39 RA000412-157 MICRO06 Non targeted RA010516-36 RA000907-56 BL000921-10 BL001221-10 ANT37-4 BL001221-4 RA000412-153 BL010320-1 Micromonas sp. RCC434 RA010516-35 MICRO01 RA000412-37 RA000907-63 MICRO07 MICRO05 0.1 + ME1-1 92/95 88/98 100/99 B C D 98/94 A Micromonas 100/100 -/- -/- -/- B -/- -/- 81/75 100/100 RA000907-39 RA000907-9 RA010613-139 -/- RA000412-36 Micromonas pusilla CCMP490 C RD010517-66 RA010412-7 -/- ANT37-3 Mantoniella Mantoniella squamata Mantoniella antarctica RCC391 Mamiella sp. Dolichomastix lepitoda 98/93 Crustomastix sp. MBIC10709 Tree from Laure paper

  7. TargetProbe Clade C (CCMP490) MICRO05 5’-UUAAUCGUCUGGACGUGG-3’ 5’-CCACGTCCAGACGATTAA-3’ Closest sequences with mismatches: Mantoniella squamata 2 mismatches Botyomyces caespitosus 3 mismatches Number of mismatches with the other Micromonas clade: 490 Vs 489 4 mismatches 490 Vs BL122 ? (more than 4)

  8. TargetProbe Clade A (CCMP489) MICRO06 5’-GCACUGGUUGGUUUUAAC-3’ 5’-GTTAAAACCAACCAGTGC-3’ Closest sequences with mismatches: Mantoniella antarctica 2 mismatches Mamiella sp 2 mismatches all BL122 clade 2 mismatches Number of mismatches with the other Micromonas clade: 489 Vs 490 3 mismatches 489 Vs BL122 2 mismatches

  9. TargetProbe Clade B (BL122) MICRO07 except 3 sequences non targeted 5’-GGACGCGCUCUGGCUUCA-3’ 5’-TGAAGCCAGAGCGCGTCC-3’ Closest sequences with mismatches: Penium margaritaceum 2 mismatches env. part. ANT 37.4 2 mismatches Number of mismatches with the other Micromonas clade: BL122 Vs 490 3 mismatches BL122 Vs 489 4 mismatches

  10. Work Plan April Tests of the probes on pure cultures July-August Application of the probes on natural samples

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