Las justificaciones desde una perspectiva evolucionista

DNA from the Tamaki River water sample was subjected to a ‘low-throughput library preparation’ protocol (Bioo-scientific NEXTFlex DNA PCR-free Sample Preparation Guide, Cat No: 514110, July 2011) prior to DNA sequencing. The DNA library was prepared by the author (as Senior Sequencing Technician) at the Massey Genome Service, Massey University, Palmerston North. To begin the mechanical shearing process, the nebulizer was attached to a small vinyl tube and 50 μl of DNA (2μg) was mixed with 700 μl of nebulisation buffer (50 % (v/v) glycerol and 50 % (v/v) TE Buffer in the nebulizer (Life Technologies; Cat No: K7025- 05). The mixture was chilled on ice for 5 minutes, then connected to a compressed air source (Nitrogen, BOC, Cat No: P1 152 28) and nebulised at 35 PSI for 6 - 8 minutes. The shearing process takes place as the nitrogen gas passes through the solution in the nebulizer. Immediately after fragmentation, the sheared DNA was purified through a ZYMO PCR purification column (Zymo Research, Cat No: D4004) ) by mixing with 2 ml of Zymo DNA binding buffer (4.2 M guanidine hydrochloride and 40% (v/v) isopropanol,) passing the mixture through a column, washing twice with 500 μl of Zymo washing buffer (1.0 M NaCL, 50mM MOPS, pH7.0, 15% (v/v) isopropanol,) and eluting in 16 μl of elution buffer (10 mM Tris-Cl, pH 8.5).

To monitor the DNA size distribution after fragmentation, the sheared products were analyzed in a Bioanalyzer (Agilent Technologies, DNA 1000 kit, Cat No: G2940CA).To start the analysis, the Bioanalyzer priming station (Agilent Technologies, Cat No: G2938-68700) (Figure 11) was set up according to the manufacturer’s protocols by aligning the syringe cap and base plate to the correct position. To prepare the gel matrix, 25μl of dye concentrate was aliquoted into the vial containing DNA gel. This was vortexed and then transferred to a spin- column and in which it was spun for 15 minutes at 6,000 rpm. For gel loading, 9 μl of gel- dye mix was aliquoted into the well-marked ‘G’ on the chip along with 5 μl of marker in the remaining wells (Figure 11). 1 μl of DNA sample was then aliquoted into the electrophoresis gel wells. 1 μl of concentrated DNA ladder was added to a separate well. The Bioanalyzer chip (Figure 11) was then vortexed at 2,400 rpm for one minute before loading onto the Bioanalyzer 2100 instrument.

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Agilent Bioanalyzer 2100 DNA Chip

Figure 11 - A) Agilent bioanalyzer priming station, B) priming station base plate aligning to a correct position

C) syringe lock clip was set to lowest position D) the DNA 1000 chip showing the position of the wells.

Once it was determined that the size of the DNA fragments was correct, the DNA was repaired by replacing the 5’ overhangs with a phosphate group to allow the ligation of the adapter and by removing the existing 3’ overhangs to create blunt ends. For end-repair, 40 μl of fragmented DNA was mixed together with 7 μl of end-repair Buffer Mix (BIOO-Scientific, NEXTFlex Cat No: 5140-05) and 3 μl of End-Repair enzyme mix (BIOO-Scientific, NEXTFlexCat No: 5142-02) and incubated in a thermocycler for 30 minutes at 22°C (Figure 12). The PCR-free protocol used an alternative method of library size selection involving the Solid Phase Reversible Immobilization (SPRI) bead system. The SPRI system uses magnetic particles (beads) coated with charged carboxyl groups that bind reversibly to DNA in the presence of polyethylene glycol (PEG) and salt (usually NaCl).

In the PCR-free protocol, the DNA was purified by collecting the beads on a magnet following successive washes and elution in a low salt buffer. The size selection process is dependent on the relative concentration of beads to DNA, where the lower the ratio, the larger will be the DNA fragments. For size selection, 160 μl of magnetic beads (Beckman Coulter Inc, Cat No: A63880) was added to the sheared DNA and washed twice with 200μl of 80% Ethanol (EtOH) before being eluted in 15 μl of elution buffer (Figure 12). Next 3.5 μl of adenylation Mix (BIOO-Scientific, NEXTFlex Cat No: 5142-02) was added into 17 μl of

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62 eluted DNA and incubated on a thermocycler for 30 minutes at 37°C (Figure 12). Following A-tailing, 31.5 μl of Ligation Mix (BIOO-Scientific, NEXTFlex Cat No: 5142-02) and 1.5 μl of DNA Index Adapter 2 (BIOO-Scientific, NEXTFlex Cat No: 514101- for Illumina compatible adapter sequences please refer to the appendix section) were added into 20.5 μl of adenylated DNA and incubated again for 15 minutes in thermocycler at 22°C prior to a post- ligation clean-up using AMPure XP beads (Figure 12). This method eliminates PCR enrichment and size selection steps which normally require an agarose gel. The fragments were quantified and checked for size distribution as before, using the BioAnalyser and the Qubit fluorometer. Prior to sequencing, the library was diluted to 9 pM which was the optimal loading concentration according to the manufacturer’s protocol (Illumina MiSeq System User Guide, Part No: 5027617 Rev. F, Nov 2012). Using the NEXTFlex protocol, the Tamaki River gDNA was successfully fragmented, end-repaired, and size-selected for 550 bp fragments.

NEXTFlex PCR-free Library Construction Steps

Figure 12 – With the NEXTFlex protocol, 1-3 μg of starting material (gDNA) is sheared to smaller fragments.

The end-repair process and size selection process are merged into a single step via the SPRI beads system that binds to the DNA accordingly to the concentration of magnetic beads. After adenylation, a new enzymatic mix is employed to enhance the adapter ligation step prior to cluster generation, without the need for a PCR enrichment step.

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