| Literature DB >> 30276031 |
Najmeh Nasiri1, Ghorbanali Nematzadeh2, Vahid Shariati-Joni3, Hamid Najafi-Zarrini4.
Abstract
PREMISE OF THE STUDY: High-yield pure chloroplast DNA (cpDNA) is necessary for whole genome sequencing. Chloroplast extraction with traditional high-salt methods causes damage to nuclei and destroys the integrity of organelles, which leads to high genomic contamination from the nucleus and mitochondria. To overcome this issue, we modified a traditional high-salt method to obtain a new approach called the NaOH low-salt method (NLS). METHODS ANDEntities:
Keywords: Poaceae; chloroplast extraction; cpDNA preparation; high‐salt methods; whole genome sequencing
Year: 2018 PMID: 30276031 PMCID: PMC6159644 DOI: 10.1002/aps3.1183
Source DB: PubMed Journal: Appl Plant Sci ISSN: 2168-0450 Impact factor: 1.936
Figure 1Diagram showing changes to classical chloroplast extraction schemes (high salt [HS] and modified high salt [mHS]) by insertion, exchange, and modification of the main steps and buffers to create a modified method (NaOH low‐salt method [NLS]). Black, blue, and red boxes refer to the HS, mHS, and NLS protocols, respectively. Buffer A = alkaline lysis; buffer B = homogenization; buffer C = washing; buffer D = dilution (see Table 1).
Reagents used in the high‐salt (HS), modified high‐salt (mHS), and NaOH low‐salt (NLS) methods
| Method | Components (buffers | Reference |
|---|---|---|
| HS | NaCl (1.25 M), Tris‐HCl (50 mM), EDTA (5 mM), BSA (0.1% w/v), β‐ME (0.1% v/v) (buffers B and D) | Bookjans et al., |
| mHS | NaCl (1.25 M), borax (0.0125 M), sodium metabisulfite (10 mM), Tris‐HCl (50 mM), EDTA (7 mM), PVP (1%), DTT (1 mM), ascorbic acid (0.25nM), BSA (0.1% w/v) (buffer B) | Shi et al., |
| NaCl (1.25 M), borax (0.0125 M), Tris‐HCl (50 mM), EDTA (7 mM), PVP (1%), DTT (1 mM), BSA (0.1% w/v) (buffers C and D) | ||
| NLS | NaOH (0.5 M), EDTA (7 mM), PVP (1 g), β‐ME (0.2% v/v) (buffer A) | This study |
| NaCl (0.62 M), Tris‐HCl (50 mM), EDTA (7 mM), PVP (2 g), DTT (1.5 mM) (buffer B) | ||
| Sorbitol (0.35 M), Tris‐HCl (50 mM), EDTA (25 mM) (buffers C and D) |
ascorbic acid = (5R)‐[(1S)‐1,2‐dihydroxyethyl]‐3,4‐dihydroxyfuran‐2(5H)‐one; β‐ME = 2‐mercaptoethanol; borax = sodium tetraborate decahydrate; BSA = bovine serum albumin; DTT = dithiothreitol; EDTA = ethylenediaminetetraacetic acid; NaCl = sodium chloride; NaOH = sodium hydroxide; PVP = polyvinylpyrrolidone; sorbitol = (2S,3R,4R,5R)‐hexane‐1,2,3,4,5,6‐hexol; Tris‐HCl = tris hydrochloride.
Buffer A = alkaline lysis; buffer B = homogenization; buffer C = washing; buffer D = dilution.
Figure 3Comparison of cpDNA purity among different chloroplast isolation methods based on the relative expression level of the target genes (gigantean, cox1, rbcL). (A) Contamination of cpDNA with nDNA. (B) Contamination of cpDNA with mtDNA. HS = high‐salt method; mHS = modified high‐salt method; NLS = NaOH low‐salt method.
Comparisons of quantity and quality of chloroplasts and cpDNAs obtained from different chloroplast extraction methods
| Method | Intactness | cpDNA spectrophotometer analysis | ||||
|---|---|---|---|---|---|---|
| Yield | Ferricyanide reduction (%) | ADP‐photophosphorylation (μM ADP mg−1 chlorophyll h−1) | DNA (ng/μL) | OD 260/280 | OD 260/230 | |
| Total DNA | — | — | — | 2130 | 1.8 | 1.7 |
| High salt | 0.7 | 49 | 488 | 890 | 1.6 | 1.9 |
| Modified high salt | 2.7 | 61.2 | 228.2 | 1437 | 2.2 | 2.5 |
| NaOH low salt | 2.4 | 85.1 | 113.1 | 342 | 1.8 | 1.2 |
— = value not measured in this sample.
Chloroplast intactness measured by ferricyanide reduction and ADP‐photophosphorylation assays.
Absorption at 625 nm wavelength.
Ratio of light absorbance at 260 and 280 nm.
Ratio of light absorbance at 260 and 230 nm.
Figure 2Isolated cpDNAs on agarose gel by three different chloroplast extraction methods (high salt [HS], modified high salt [mHS], and NaOH low‐salt method [NLS]; 1‐kbp DNA ladder [SM0311, Fermentas International Inc., Burlington, Ontario, Canada]).
Figure 4Brightfield and fluorescent microscopy images of isolated chloroplasts using the modified high‐salt isolation method (A) and the NaOH low‐salt isolation method (B). Results of chlorophyll fluorescence analysis are shown for each method: (i) chlorophyll red autofluorescence; (ii) phase contrast, zoom‐in views; (iii) chlorophyll fluorescence analysis after CFDA staining. (C) Chloroplast fractions obtained from each isolation method after centrifuging on a Percoll density gradient (40%).
Depth of coverage estimation of Aeluropus littoralis cpDNA aligned reads based on the reference genomes and target genes
| Gene/Genome | Chloroplast reference genome | Mitochondrial reference genome | Target genes | ||
|---|---|---|---|---|---|
|
|
|
| |||
| No. of total reads | 8,745,956 | 8,745,956 | 8,745,956 | 8,745,956 | 8,745,956 |
| No. of mapped reads | 3,986,432 | 4538 | 1729 | 6 | 52,042 |
| Mapped bases (bp) | 597,964,854 | 680,701 | 208,768 | 840 | 6,552,714 |
| Reference length (bp) | 135,737 | 468,628 | 420 | 618 | 1412 |
| Sequencing depth (×) | 4405 | 1 | 497 | 2 | 4640 |
Astrebla pectinata.
Sorghum bicolor.
| Species | Voucher specimen accession no. | Collection locality |
|
|---|---|---|---|
|
| MMI‐001‐NN | Mazandaran, Miankaleh | 20 |
|
| MSI‐002‐NN | Mazandaran, Sari | 6 |
|
| MSI‐003‐NN | Mazandaran, Sari | 6 |
|
| KRM‐004‐NN | Khorasan razavi, Mashhad | 6 |
|
| MSI‐005‐NN | Mazandaran, Sari | 3 |
N = number of individuals; NN = Najmeh Nasiri, collector.
Vouchers deposited at the Germplasm Bank, Genetic and Agricultural Biotechnology Institute of Tabarestan, University of Agricultural Sciences and Natural Resources, Sari, Iran.
Locality and Iranian province.