Name: optimization and comparative analysis of plant organellar dna enrichment methods suitable for next-generation sequencing
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Vi skulle vilja erkänna finansiering från Förenta staternas avdelningen för jordbruk och jordbruksforskning och från National Science Foundation (IOS 1025881 och IOS 1361554). Vi tackar R. Caspers för växthusunderhåll och växtvård. Vi tackar också Universitetet i Minnesota Genomics Center, där Illumina biblioteket förberedelser och sekvensering utfördes. Vi är också tacksamma för kommentarerna från tidningsredaktörerna och fyra anonyma granskare som ytterligare förstärkt vårt manuskript. Vi tackar också OECD för ett stipendium till SK för att integrera dessa protokoll för samarbetsprojekt med kollegor i Japan.

1. Generering av växtmaterial för organellärisolering och DNA-extraktion <ol><li> Standardväxt av veteplanter <ol><li> Växtfrön i vermikulit i små, fyrkantiga krukor med 4-6 frön per hörn. Överföring till växthus eller växthus med 16 h ljuscykel, 23 ºC dag / 18 ºC natt. </li><li> Vattna växterna varje dag. Gödda plantorna med ¼ tsk granulärt 20-20-20 NPK-gödselmedel vid spiring och vid 7 dagar efter spiring. </li></ol></li><li> Alternativ etiolering av veteplanter ...

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	<li>Liberatore, K. L., Dukowic-Schulze, S., Miller, M. E., Chen, C., Kianian, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+mitochondria+in+plant+development+and+stress+tolerance.">The role of mitochondria in plant development and stress tolerance.</a> Free Radic Biol Med. 100, 238-256 (2016).</li><li>Samaniego Castruita, J. A., Zepeda Mendoza, M. L., Barnett, R., Wales, N., Gilbert, M. 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Hittills är de flesta organellära sekvenseringsstudier centrerad på traditionella DC-metoder för att berika för specifikt DNA. Metoder för att isolera organeller från olika växter har beskrivits, inklusive moss 40 ; Monokoter såsom vete 15 och havre 11 ; Och dikotes som arabidopsis 11 , solros 17 och rapsfrö 14 . De flesta protokoll fokuserar på bladvävnad <sup class...

<html> Genomsekvensering är ett kraftfullt verktyg för att dissekera den underliggande genetiska grunden för viktiga växtegenskaper. De flesta genom-sekvensstudierna fokuserar på kärngenominnehållet, eftersom majoriteten av gener ligger i kärnan. Organella genomer, inklusive mitokondrier (över eukaryoter) och plastider (i växter, den specialiserade formen, kloroplasten, arbetar med fotosyntes) bidrar emellertid med väsentlig genetisk information som är väsentlig för organismutveckling, stressrespons och övergripande fitness 1 . Organellärgener ingår typiskt i totala DNA-extraktioner avsedda för kärngenom-sekvensering, även om metoder för att reducera organelltal före DNA-extraktion också används 2 . Många studier har använt sekvenseringsresultat från totala gDNA-extraktioner för att samla organellära genom 3 , 4 , 5 ,Xref &quot;&gt; 6 , 7. Men när målet för studien är att fokusera på organella genomer, ökar sekvenseringskostnaderna eftersom många läsningar är&quot; förlorade &quot;till kärn-DNA-sekvenserna, speciellt i växter med stora kärnvätskor På grund av dubbelarbete och överföring av organella sekvenser i kärngenomet och mellan organeller, är det dessutom en lösning av den korrekta mapppositionen för sekvensering som läser till det ordnade genomet bioinformatiskt utmanande 2 , 8. Rening av organella genomerna från kärngenometet är en Strategi för att minska dessa problem. Ytterligare bioinformatikstrategier kan användas för att separera läser den kartan till regioner med homologi mellan mitokondrier och kloroplaster. Medan organellärgenerna från många växtarter har sekvenserats, är lite känt om bredden av organellär genom diversitetTillgänglig i vilda populationer eller odlade avelspooler. Organellärgener är också kända för att vara dynamiska molekyler som genomgår signifikant strukturell omläggning på grund av rekombination mellan repetitionssekvenserna 9 . Dessutom finns flera kopior av organellärgenomet inom varje organell, och flera organeller finns inom varje cell. Inte alla kopior av dessa genomer är identiska, vilket är känt som heteroplasmi. I motsats till den kanoniska bilden av &quot;mästarkretsar&quot; finns det nu växande bevis för en mer komplex bild av organellära genomstrukturer, inklusive sub-genomiska cirklar, linjära kromosomer, linjära concatamerar och grenade strukturer 10 . Sammansättningen av växtorganella genomer kompliceras ytterligare av deras relativt stora storlekar och väsentliga inverterade och direkta upprepningar. Traditionella protokoll för organellär isolering, DNA-rening och efterföljande genom<html> E-sekvensering är ofta besvärlig och kräver stora volymer vävnadsinmatning, med flera gram uppåt i hundratals gram unga bladvävnader som är nödvändiga som utgångspunkt 11 , 12 , 13 , 14 , 15 , 16 , 17 . Detta gör organellärgenomsekvensering otillgänglig när vävnaden är begränsad. I vissa situationer är frömängderna begränsade, till exempel när det är nödvändigt att sekvensera generationsbaserade eller i manliga sterila linjer som måste bibehållas genom korsning. I dessa situationer kan organellär DNA renas och sedan utsättas för helgenomförstärkning. Hela genom-amplifiering kan emellertid introducera signifikant sekvenseringsförspänning, vilket är ett speciellt problem vid bedömning av strukturell variation, sub-genomiska strukturer och heteroplasminsnivåer&gt; 18. Nya framsteg i bibliotekets förberedelse för kortläsning av sekvenseringsteknologier har övervunnit låga ingångsbarriärer för att undvika helgenomförstärkning. Till exempel tillåter Illumina Nextera XT-biblioteksberedningssatsen så lite som 1 ng DNA att användas som ingång 19 . Standardbiblioteksberedningar för långlästa sekvenseringsapplikationer, såsom PacBio eller Oxford Nanopore-sekvenseringsteknologi, kräver emellertid fortfarande en relativt hög mängd ingångs-DNA, vilket kan utgöra en utmaning för organellär genom-sekvensering. Nyligen har nya användarbaserade, långläsna sekvenseringsprotokoll utvecklats för att reducera ingångsmängderna och för att underlätta genomsekvensering i prover där man erhåller mikrogrammängder av DNA svårt 20 , 21 . Att erhålla högmolekylära vikt, rena organellära fraktioner för att mata in i dessa bibliotekspreparationer är emellertid en utmaning. Vi sökte tO jämföra och optimera organellära DNA-anriknings- och isoleringsmetoder som är lämpliga för NGS utan behov av hel-genom-amplifiering. Specifikt var vårt mål att bestämma bästa praxis för att berika för organellärt DNA med hög molekylvikt från begränsade utgångsmaterial, såsom ett prov av ett blad. Detta arbete presenterar en jämförande analys av metoder för att berika för organellär DNA: (1) ett modifierat, traditionellt differentialcentrifugeringsprotokoll kontra (2) ett DNA-fraktioneringsprotokoll baserat på användningen av en kommersiellt tillgänglig DNA-CpG-metylbindningsdomänprotein 22 applicerad på växtvävnad 23 . Vi rekommenderar bästa praxis för isolering av organellär DNA från vävnadslövvävnad, som lätt kan utvidgas till andra växter och vävnader.

<table border="0" cellpadding="0" cellspacing="0" width="685">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">2-mercaptoethanol (beta-mercaptoethanol; BME)</td>
			<td style="width:183px;">Sigma Aldrich</td>
			<td style="width:119px;">M3148-100ml</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">2-propanol (Isopropyl alcohol/isopropanol), bioreagent</td>
			<td>Sigma Aldrich</td>
			<td>I9516</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">agarose, Bio-Rad Cetified Megabase agarose</td>
			<td>Bio-Rad</td>
			<td>1613108</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">analytical balance</td>
			<td>Mettler Toledo</td>
			<td>AB54-S</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">balance</td>
			<td>Mettler Toledo</td>
			<td>PB1502-S</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">bovine serum albumin (BSA)</td>
			<td>Sigma Aldrich</td>
			<td>B4287-25G</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Ceramic grinding cylinders, 3/8in x 7/8in</td>
			<td>SPEX SamplePrep</td>
			<td>2183</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Cryogenic Blocks compatible with tissue homogenizer for holding 50 ml tubes</td>
			<td>SPEX SamplePrep</td>
			<td>2664</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DNaseI</td>
			<td>Sigma</td>
			<td>DN25</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ethanol, absolute</td>
			<td>Decon Laboratories</td>
			<td>2716</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Ethylenediamine Tetraacetic Acid (EDTA), 0.5M Solution, pH8.0</td>
			<td>Fisher</td>
			<td>BP2482-500</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">gel imaging system</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">gel stain</td>
			<td></td>
			<td></td>
			<td style="width:167px;">Such as GelRed or Ethidium Bromide</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">grinding pestle, wide tip for 2 ml conical tubes</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Guanidine-HCl, 8M solution</td>
			<td>ThermoFisher</td>
			<td>24115</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">LightCycler 480 SYBR Green I Master</td>
			<td>Roche</td>
			<td>4707516001</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">liquid nitrogen</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Lysing enzymes from Trichoderma harzianum</td>
			<td>Sigma</td>
			<td>L1412</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Magnesium Chloride</td>
			<td>G Bioscience</td>
			<td>24115</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">magnetic rack</td>
			<td>ThermoFisher</td>
			<td>A13346</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">microcentrifuge tubes, LoBind 1.5 ml&#160;</td>
			<td>Eppendorf</td>
			<td>22431021</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">microcentrifuge tubes, standard nuclease-free 1.5 ml</td>
			<td>Eppendorf</td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="120">
			<td height="120" style="height:120px;width:216px;">microcentrifuge, refrigerated</td>
			<td>Sorvall&#160;</td>
			<td>Legend X1R</td>
			<td style="width:167px;">Or equivalent product, must be capable of reaching at least 18,000 x g with rotors for 50 ml tubes, Oak Ridge tubes, and 1.5 ml tubes</td>
		</tr>
		<tr height="120">
			<td height="120" style="height:120px;width:216px;">microcentrifuge, room temperature</td>
			<td>Eppendorf</td>
			<td>5424</td>
			<td style="width:167px;">Or equivalent product, must be capable of reaching at least 18,000 x g with rotor for 1.5 ml and 2 ml microcentrifuge tubes</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Microcon DNA Fast Flow Centrifugal Filter Units</td>
			<td>EMD Millipore</td>
			<td>MRCFOR100</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Miracloth, 1 square per sample cut to fit funnel</td>
			<td>EMD Millipore</td>
			<td>475855</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NEBNext Microbiome DNA Enrichment Kit</td>
			<td>New England Biolabs</td>
			<td>E2612L</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">parafilm</td>
			<td>Parafilm M</td>
			<td>PM992</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">plastic pots and trays</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">polyvinylpyrrolidone (PVP)</td>
			<td>Fisher</td>
			<td>BP431-100</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Proteinase K</td>
			<td>Qiagen</td>
			<td>19131</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pulsed-Field Gel Electrophoresis rig (e.g. CHEF DR III)</td>
			<td>Bio-Rad</td>
			<td>1703697</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">purification beads, Agencourt AMpureXP beads</td>
			<td>Beckman Coulter</td>
			<td>A63881</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">QIAamp DNA Mini Kit</td>
			<td>Qiagen</td>
			<td>51304</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Qiagen 20/g Genomic Tip DNA Extraction Kit</td>
			<td>Qiagen</td>
			<td>10223</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qiagen Buffer EB (elution buffer)</td>
			<td>Qiagen</td>
			<td>19086</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Qiagen DNA Extraction Buffer Set</td>
			<td>Qiagen</td>
			<td>19060</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">QiaRack</td>
			<td>Qiagen</td>
			<td>19015</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">qPCR machine (e.g. Roche Light Cycler 480)</td>
			<td>Roche</td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">qPCR plate sealing film</td>
			<td>Roche</td>
			<td>4729757001</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">qPCR plate, 96 well plate</td>
			<td>Roche</td>
			<td>4729692001</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qubit&#160;assay tubes</td>
			<td>Life Technologies</td>
			<td>Q32856</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qubit Broad Spectrum assay kit</td>
			<td>Life Technologies</td>
			<td>Q32850</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qubit High Sensitivity assay kit</td>
			<td>Life Technologies</td>
			<td>Q32851</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">RNaseA</td>
			<td>Qiagen</td>
			<td>19101</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Serological pipettes (20 ml) and pipet-aid</td>
			<td>Fisher</td>
			<td>13-678-11</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Small funnels, 1 per sample</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Sodium Chloride</td>
			<td>Ambion</td>
			<td>AM9759</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Soft paintbrush, 2 per sample</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="260">
			<td height="260" style="height:260px;width:216px;">SPEX SamplePrep 2010 Geno/Grinder or another type of tissue homogenizer</td>
			<td>SPEX SamplePrep</td>
			<td></td>
			<td style="width:167px;">Or another comparable tissue homogenizer. If you do not have access to a tissue homogenizer, then grinding in a pre-chilled mortar and pestle will suffice (see protocol for details). However, a homogenizer will give more consistent results and total homogenization time is reduced.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Sucrose</td>
			<td>Omnipure</td>
			<td>8550</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">TBE</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">thermomixer</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Tris</td>
			<td>Sigma</td>
			<td>T2819-100ml</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Triton X-100</td>
			<td>Promega</td>
			<td>H5142</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">tube rotater</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">tubes, 50 mL conical polypropylene</td>
			<td>Corning</td>
			<td>352070</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">tubes, 50 ml high-speed polypropylene&#160;</td>
			<td>ThermoScientific/Nalgene</td>
			<td>3119-0050</td>
			<td style="width:167px;">e.g. Nalgene Oakridge tubes or equivalent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">vermiculite</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">water bath</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">water, sterile and certified Nuclease-free&#160;</td>
			<td>Fisher</td>
			<td>1481</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">water, sterile milliQ</td>
			<td></td>
			<td></td>
			<td style="width:167px;"></td>
		</tr>
	</tbody>
</table>

optimization and comparative analysis of plant organellar dna enrichment methods suitable for next-generation sequencing

Plantorganella genomer innehåller stora, repetitiva element som kan genomgå parning eller rekombination för att bilda komplexa strukturer och / eller subgenomiska fragment. Organellärgener finns också i tillsatser inom en given cell eller vävnadstyp (heteroplasm), och en överflöd av subtyper kan förändras under utveckling eller vid stress (substökiometrisk växling). Nästa generationens sequencing (NGS) -teknologi krävs för att få en djupare förståelse av organellär genomstruktur och funktion. Traditionella sekvenseringsstudier använder flera metoder för att erhålla organellärt DNA: (1) Om en stor mängd startvävnad används, homogeniseras den och utsätts för differentiell centrifugering och / eller gradientrening. (2) Om en mindre mängd vävnad används ( dvs. om frön, materialet eller utrymmet är begränsat) utförs samma process som i (1), följt av hel-genom-amplifiering för att erhålla tillräckligt med DNA. (3) Bioinformatikanalys kan användas för att sökaDet totala genomiska DNA: n och att analysera organellärläsning. Alla dessa metoder har inneboende utmaningar och avvägningar. I (1) kan det vara svårt att erhålla en så stor mängd startvävnad; I (2) kan helgenomförstärkning införa en sekvenseringsförspänning; Och i (3) kan homologi mellan kärn- och organellära genomer störa sammansättning och analys. I växter med stora kärnämnen är det fördelaktigt att berika för organellär DNA för att minska sekvenseringskostnader och sekvenskomplexitet för bioinformatikanalyser. Här jämför vi en traditionell differentialcentrifugeringsmetod med en fjärde metod, en anpassad CpG-metyl-pulldown-tillvägagångssätt, för att separera det totala genomiska DNA-värdet i kärn- och organellära fraktioner. Båda metoderna ger tillräckligt med DNA för NGS, DNA som är högt berikat för organellära sekvenser, om än i olika förhållanden i mitokondrier och kloroplaster. Vi presenterar optimeringen av dessa metoder för vävnadslövvävnad och diskuterar stora fördelar och dNackdelar med varje tillvägagångssätt i samband med provingång, protokolllättnad och nedströmsapplikation.

De protokoll som presenteras i detta manuskript beskriver två separata metoder för att berika för organellär DNA från växtvävnad. Villkoren som presenteras här återspeglar optimering för vetevävnad. En jämförelse av nyckelsteg i protokollen, obligatorisk vävnadsingång och DNA-utmatning beskrivs i figur 1 . Stegen i det DC-protokoll som vi testat följer liknande förhållanden som de som beskrivits tidigare ( Figur 1A</str...

Watch this Scientific Journal Video about Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing at JoVE.com

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Jämförelsen och optimeringen av två organellära DNA-berikningsmetoder presenteras: traditionell differentiell centrifugering och fraktionering av det totala gDNA baserat på metyleringsstatus. Vi bedömer den resulterande DNA-kvantiteten och kvaliteten, demonstrerar prestanda vid kortläsning av nästa generationens sekvensering och diskuterar potentialen för användning vid långlästsekvens med en molekylsekvensering.

Optimering och jämförande analys av organellära DNA-berikningsmetoder lämpliga för nästa generations sekvensering

Plant organellar genomes contain large, repetitive elements that may undergo pairing or recombination to form complex structures and/or sub-genomic ...

The overall goal of this experiment is to compare two methods used to isolate high quality organellar DNA, both plastid and mitochondria DNA from plant leaf tissue that is suitable for next-generation sequencing. These methods can help answer key questions in plant biology such as the extent of organellar diversity across taxa and how changes in organellar genome sequence or structure affect development and stress response. We will compare two techniques, the differential centrifugation method that enriches for one specific organellar type and the meta fractionation technique that recovers total organellar DNA from smaller frozen tissue samples.The standard procedure for growing wheat seedlings, is to plant seeds in vermiculite, in square pots with four to six seeds per corner. Transfer the pots to a greenhouse with a 16 hour light cycle. Water the plants each day.Fertilize the plants with one quarter teaspoon of granular 20-20-20 MPK fertilizer upon germination, and again at seven days post germination. For adulation of wheat seedlings, plant seeds and care for plants as in the standard procedure. But place the pots in a dark growth chamber.An alternative to growing these seedlings at a dark growth chamber is to cover the plants in the greenhouse but with proper ventilation. The first step in this procedure is to isolate the organelles. Harvest five grams of fresh tissue and rinse it in cold, sterile water in a chilled beaker on ice.Using scissors, cut the leaf tissue into approximately one centimeter pieces directly into a pre-chilled 50 millimeter tube containing two ceramic grinding cylinders. Keep the samples on ice throughout the procedure. To avoid cross-contamination, it is important to change the scissors between samples.Take the samples to the fume hood and add 20 milliliters of STE buffer to each 50 milliliter tube. Place the samples into pre-chilled cryogenic grinding blocks in a tissue grinding apparatus and grind the samples for 30 seconds at 1, 750 rotations per minute. Place the samples on ice for about one minute.Rotate the sample positions and grind for another 30 seconds at 1, 750 rotations per minute. Return the samples to the ice bucket. For each sample, insert a funnel into a clean 50 milliliter tube placed in ice and place one layer of filtration cloth into the funnel.Pre-wet the filtration cloth with five milliliters of STE buffer and save the flow through. Pour the homogenized tissue into the funnel. Rinse the grinding tube with 15 milliliters of STE buffer, recap and invert the tube to rinse walls and lid and pour its contents into the funnel.Carefully remove the ceramic stones and then squeeze and wring out the filtration cloth into the funnel. To avoid cross-contamination, change gloves between samples. Wrap the tube caps with paraffin film to avoid spillage.Centrifuge at 2, 000 x G, at four degree celsius for 10 minutes. Next, use a serological pipette to carefully aspirate the supernatant without disturbing the pellet and place it in a 50 milliliter high speed centrifuge tube with a tight sealing gasket. Place a small beaker of ice on a scale, tear the scale and weigh each supernatant.Use STE buffer to balance the tubes to within 0.1 grams and then centrifuge at 18, 000 x G in four degree celsius for 20 minutes. When the centrifugation is complete, return samples to the fume hood and discard the supernatant. Add one milliliter of ST buffer to the pellet and resuspend gently using a soft paintbrush.Add 24 milliliters of ST buffer to get a final volume of 25 milliliters. Gently swirl the paintbrush around in a suspension to mix, and then press the paintbrush on the side of a tube to remove all liquid before removing the paintbrush. After balancing the tubes, centrifuge at 18, 000 x G in four degree celsius for 20 minutes.During this centrifugation, prepare DNA's 1 solution as described in the text protocol and aliquot 200 microliters to a 1.5 milliliter tube per sample. When the centrifugation is complete, discard the supernatant and blot the tube. To each high speed centrifuge tube, add 300 microliters of STE buffer and resuspend the pellet using a soft paint brush.Place the paint brush in the previously prepared 1.5 milliliter tube containing 200 microliters of DNA's 1 solution and swirl the paint brush to remove any residual pellet stuck in the brush. Pipette the DNA's 1 solution into the high speed centrifuge tube and gently swirl to mix. Wrap paraffin film around the top of each tube and incubate at 37 degrees celsius in a water bath for 30 minutes.During the incubation, gently mix by swirling. Using a pipette tip with a wide orifice, gently pipette the pellet mixture out of the tube and place it in a 1.5 milliliter low binding tube. Add 500 microliters of 400 millimolar EDTA, pH 8.0 to the high speed centrifuge tube.Gently pipette to completely remove the residual pellet and transfer the EDTA to the low binding tube containing the pellet mixture. Gently mix by inversion. Centrifuge at 18, 000 x G, at four degree celsius for 20 minutes.Subsequently, discard the supernatant, blot each tube and use the pellet immediately for DNA isolation. In this method, organellar DNA is enriched from total genomic DNA that was extracted using commercial DNA extraction columns. Prepare the required amount of MBD2 FC protein bound magnetic beads, per the manufacturer's instructions and scale the reactions to use between one and two micrograms of total input DNA.In this demonstration, 160 microliters of beads is required for one microgram of total input DNA. To capture methylated nuclear DNA, add one microgram of input DNA to a tube containing 160 microliters of MBD2 bound magnetic beads for each individual sample and gently pipette up and down with a wide bore tip. Add the appropriate volume of 5x bind wash buffer for a final concentration of 1x and pipette the sample up and down with a wide bore tip, a few times to mix.Rotate the tubes at room temperature for 15 minutes. For the success of the pull down, it is critical to thoroughly mix the beads during the incubation, particularly, if there is significant bead clumping. To prevent bead clumping and to ensure pull down of the methylated DNA, gently pipette the samples with a wide bore pipette tip and flick the samples two to three times throughout the incubation.Briefly spin the tubes containing the DNA and magnetic bead mixture. Place the tubes on a magnetic rack for at least five minutes to collect the beads to the side of the tubes. The solution should appear clear, it contains un-methylated organellar enriched DNA.Using wide bore tips, carefully remove the cleared supernatant without disturbing the beads and transfer the supernatant to a clean, low binding two milliliter microcentrifuge tube. Store the samples at 20 or 80 degrees celsius. Acute PCR assay was employed to assess the relative abundances of three organelle specific implicons in total genomic DNA and the organellar DNA fraction obtained from both methods.Overall, the data indicate that the differential centrifugation method, preferentially enriches for mitochondria. The unmethylated fraction of the methylfractionated total genomic DNA, shows substantial enrichment of both organellar implicons. Percentages of reads mapped to the mitochondria or chloroplast chinese spring and chris cultivated wheat reference genomes are consistent with the QPCR results.Differential centrifugation yield DNA that is more enriched in mitochondria DNA and methylfractionation yields DNA that likely reflects the native abundance of the two organellar genomes. Sample labels including E, designate idyllated samples and NE designate non-idyllated samples. Interestingly, idyllation did not change organellar abundances.In both methods, the theoretical coverage of the mitochondria or chloroplast referenced genomes, exceeds 100x coverage, even when 12 libraries atremultiplexed. The total genomic DNA migrates as a diffused smear in post field gel electrophoresis and exceeds 50 kilobases. The nuclear fraction after methylfractionation decreases in size, but remains centered around 50 kilobases, suggesting that methylfractioanted DNA is most suitable for long read sequencing.Once mastered, both organellar DNA extraction techniques can be done in one to two days, from sample collection to assessment of final product, if performed properly. The methylfractionation technique has the potential to greatly expand the range of organellar DNA studies to rare and difficult samples, since tissue inputs are extremely low. However, differential centrifugation may still be preferable when solely mitochondria DNA is required for downstream studies.Likewise, centrifugation steps maybe adjusted to preferentially extract plastid DNA if desired. Both organellar DNA extraction methods yield DNA that is suitable for next generation sequencing but methylfractionation yields high molecular rate DNA that is ideal for long read sequencing.

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Använda CyVerse Resources för<em&gt; De Novo</em&gt; Jämförande transkriptomik av obehandlade (icke-modellerade) organismer

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative ...

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Bedömning av DNA kontaminering i RNA-prover baserat på Ribosomal DNA

One method extensively used for the quantification of gene expression changes and transcript abundances is reverse-transcription quantitative real-time ...

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Rening av hög molekylvikt Genomiskt DNA från mjöldagg för lång Läs Sequencing

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics ...

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA isolering och hög genomströmning sekvensering bibliotek konstruktion för herbarieexemplar

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with ...

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Riktade nästa generations sekvensering och bioinformatik Pipeline för att utvärdera genetiska determinanter av konstitutionella sjukdom

Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The ...

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Detektion av sällsynta händelser med fel-korrigerade DNA och RNA-sekvensering

Conventional next-generation sequencing techniques (NGS) have allowed for immense genomic characterization for over a decade. Specifically, NGS has been ...

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Förstärkning av nära fullängds HIV-1 Proviruses för nästa generations sekvensering

The Full-Length Individual Proviral Sequencing (FLIPS) assay is an efficient and high-throughput method designed to amplify and sequence single, near ...

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Hög genomströmning identifiering av reglerande gensekvenser som använder nästa generations sekvensering av cirkulär kromosom konformation fånga (4C-seq)

The identification of regulatory elements for a given target gene poses a significant technical challenge owing to the variability in the positioning and ...

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA nästa generations sekvensering och en bioinformatik pipeline för att identifiera uttryckta LINE-1s på Locus-specifik nivå

Long INterspersed Elements-1 (LINEs/L1s) are repetitive elements that can copy and randomly insert in the genome resulting in genomic instability and ...