Log In Sign up
The largest database of trusted experimental protocols
> Chemicals & Drugs > Nucleic Acid > Chloroplast DNA

Chloroplast DNA

Chloroplast DNA (cpDNA) refers to the genetic material found within the chloroplasts of plant and algal cells.
Chloroplasts are organelles responsible for photosynthesis and contain their own circular DNA molecules, distinct from the nuclear genome. cpDNA is maternally inherited, haploid, and contains genes related to photosynthesis, metabolism, and other essential chloroplast functions.
Analyzing cpDNA can provide insights into plant evolution, phylogenetics, and genetic diversity.
Researchers can optimze their cpDNA analysis using PubCompare.ai, an AI-driven research protocol platform that helps locate the best methods from literature, preprints, and patents.
This streamlines the research process and helps scientists find the most effective techniques for their chloroplast DNA projects.
Experence the power of AI-driven protocol selection with PubCompare.ai.

Most cited protocols related to «Chloroplast DNA»

1
Chloroplast DNA sequencing protocol
After the cpDNA isolation with modified high salt method, approximately 5–10 µg of DNA was sheared, followed by adapter ligation and library amplification, subjecting to Illumina Sample Preparation Instructions. The fragmented cpDNAs were sequenced at both single-read using the Illumina Genome Analyzer IIx platform at the in-house facility at The Germplasm Bank of Wild Species in Southwestern China. The obtained paired-end reads (2×100 bp read lengths) were assembled to the reference genome sequence to roughly estimate the genome coverage and cpDNA purity (the reads aligned to the reference genome sequence were served as cpDNA sequence) using the software program Geneious version 4.7 [20] . The reference chloroplast genome sequence of O. nivara (NC_005973) and P. persica (NC_014697) were downloaded from GenBank.
Shi C., Hu N., Huang H., Gao J., Zhao Y.J, & Gao L.Z. (2012). An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing. PLoS ONE, 7(2), e31468.
Full text: Click here
Publication 2012
Chloroplast DNA DNA Library Genome Genome, Chloroplast Germplasm Bank isolation Ligation Salts
2
Maize Genomic DNA Preparation for SMRT Sequencing
DNA samples for SMRT sequencing were prepared using maize inbred line B73 from NCRPIS (PI550473), grown at University of Missouri. Seeds of this line were deposited at NCRPIS (tracking number PI677128). Etiolated seedlings were grown for 4–6 days in Pro-Mix at 37 °C in darkness to minimize chloroplast DNA. Batches of ~10 g were snap-frozen in liquid nitrogen. DNA was extracted following the PacBio protocol ‘Preparing Arabidopsis Genomic DNA for Size-Selected ~20 kb SMRTbell Libraries’ (http://www.pacb.com/wp-content/uploads/2015/09/Shared-Protocol-Preparing-Arabidopsis-DNA-for-20-kb-SMRTbell-Libraries.pdf).
Genomic DNA was sheared to a size range of 15–40 kb using either G-tubes (Covaris) or a Megarupter device (Diagenode), and enzymatically repaired and converted into SMRTbell template libraries as recommended by Pacific Biosciences. In brief, hairpin adapters were ligated, after which the remaining damaged DNA fragments and those without adapters at both ends were eliminated by digestion with exonucleases. The resulting SMRTbell templates were size-selected by Blue Pippin electrophoresis (Sage Sciences) and templates ranging from 15 to 50 kb, were sequenced on a PacBio RS II instrument using P6-C4 sequencing chemistry. To acquire long reads, all data were collected as either 5- or 6-h sequencing videos.
Jiao Y., Peluso P., Shi J., Liang T., Stitzer M.C., Wang B., Campbell M.S., Stein J.C., Wei X., Chin C.S., Guill K., Regulski M., Kumari S., Olson A., Gent J., Schneider K.L., Wolfgruber T.K., May M.R., Springer N.M., Antoniou E., McCombie W.R., Presting G.G., McMullen M., Ross-Ibarra J., Dawe R.K., Hastie A., Rank D.R, & Ware D. (2017). Improved maize reference genome with single-molecule technologies. Nature, 546(7659), 524-527.
Full text: Click here
Publication 2017
Arabidopsis Chloroplast DNA Darkness Digestion DNA Damage Electrophoresis Exonuclease Freezing Genome Genomic Library Maize Medical Devices MEV protocol NCOR2 protein, human Nitrogen Plant Embryos Seedlings
3
Evaluating DNA Polymerase Fidelity in GS20 Sequencing
The GS20 emPCR process incorporates the use of the high-fidelity polymerase, Platinum Taq Hifidelity (Invitrogen), an enzyme mixture composed of recombinant Taq DNA polymerase, Pyrococcus spp. GB-D thermostable polymerase and Platinum Taq antibody. This enzyme is marketed partly on its very low misincorporation rate, 2 × 10−6 (Invitrogen). In this study we find the actual rate of misincorporation to be higher (≈7 × 10−4), similar to results from a previous aDNA study that has also specifically examined these properties of this enzyme (8 (link)). To discriminate between true aDNA damage and enzyme error or potential damage that may have arisen during the DNA extraction or that may have been present in the DNA before extraction, we analysed a further dataset of GS20 sequences, generated from a modern DNA extract, comprising 390 965 bp of L.tulipfera cpDNA. These data are part of the first chloroplast genome sequenced using the GS20 (J.E. Carlson, J.H. Leebens-Mack and D.G. Peterson, manuscript in preparation) and constitutes all the sequence reads between np 45 000 and 90 000 of the genome (J.E. Carlson, J.H. Leebens-Mack and S. Schuster, unpublished data). Although we are aware that in theory some complications may be envisioned when comparing cpDNA with mtDNA, at the current time there is a paucity of available datasets that contain sufficiently large amounts of sequence data to enable meaningful statistical comparisons. Thus this dataset provides the most suitable information at this time. The data analysed here have maximal coverage of 36 times, with a mean and modal coverage of 8.7 and 8 times, respectively. The L.tulipfera cpDNA sequences are available at the NCBI Trace Archives (Trace Identifiers 1367656065–1367659980). Analysis of the genomic data produced indicates that levels of heteroplasmy in the sample are negligible, thus unlikely to effect the analyses (J.E. Carlson, J.H. Leebens-Mack and S. Schuster, unpublished data). Furthermore, as DNA from this sample was freshly extracted from modern tissue, miscoding lesions observed in the data are unlikely to be due to anything other than PCR or other sequencing error that arises during the GS20 data production process. The miscoding lesion spectrum was extracted from the data in the same manner as applied to the mtDNA data. For data summary see Table 1.
A χ2-test of independence was used to investigate whether the distribution of miscoding lesions was the same in the mammoth and chloroplast sequence data. The data were first summarized into six complementary damage pairs (Table 1). Subsequently, because nucleotide usage is different between the mammoth and chloroplast data, tests were performed separately on those miscoding lesions that originated from an A or T (A+T), and those that originated from a G or C (G+C).
Gilbert M.T., Binladen J., Miller W., Wiuf C., Willerslev E., Poinar H., Carlson J.E., Leebens-Mack J.H, & Schuster S.C. (2006). Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research, 35(1), 1-10.
Publication 2006
Chloroplast DNA Chloroplasts DNA, Ancient DNA, Mitochondrial Enzymes GB-D polymerase Genome Genome, Chloroplast Heteroplasmy Immunoglobulins Mammuthus Nucleotides Platinum Pyrococcus Taq Polymerase Tissues
4
Estimating Bisulfite Conversion Rate in WGBS
Sodium bisulfite converts unmethylated cytosines in DNA molecules to uracils, which are read out as thymines during sequencing. However depending on the treatment time and/or experimental conditions, the conversion may not be complete, leaving certain unmethylated cytosines as C’s. The bisulfite conversion rate, defined as the rate at which unmethylated cytosines in the sample appear as T’s in the sequenced reads, is an important measure of the quality of a WGBS experiment. Estimating bisulfite conversion rate requires a priori knowledge of the methylation status on at least a portion of the cytosines in the sample. One typical technique is to spike in some DNA that is known to be unmethylated, such as a Lambda virus, when preparing sequencing libraries. Alternatively, one may use other unmethylated cytosines, such as the those in chloroplast DNA of plants or mitochondrial DNA of humans [32] (link). We count the number of converted reads (containing T’s) and the total number of reads covering those unmethylated cytosines. The ratio of converted reads to all reads gives the estimates of the bisulfite conversion rate. The method is implemented in the bsrate program.
Song Q., Decato B., Hong E.E., Zhou M., Fang F., Qu J., Garvin T., Kessler M., Zhou J, & Smith A.D. (2013). A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics. PLoS ONE, 8(12), e81148.
Full text: Click here
Publication 2013
Chloroplast DNA Cytosine DNA, Mitochondrial Homo sapiens hydrogen sulfite Methylation Plants sodium bisulfite Thymine Uracil Virus
5
Curation of Organelle Genome Databases
The protein reference sequence database was entirely revised for PREPACT 2.0 and now relies on translated coding sequences of full organelle genomes taking known editing events into account. Original GenBank accessions (Table 1) were retrieved from NCBI, split into their various elements such as header, feature list, qualifiers and sequence origin and saved into the internal MySQL database after format checking. The fully-functional hierarchical tree of feature and qualifier objects within sequence objects is retained. A complete set of associated methods for position calculation, information retrieval and manipulation within PREPACT 2.0 makes it possible to check for potentially erroneous feature locations, translational mismatches and CDS naming issues during subsequent revision where necessary. Flexible regular expression-based search and replace classes scanning the sequence entries for necessary modifications are stored on a per-accession basis to curate the available organellar genomes. When present, annotated editing sites were parsed from the different formats currently present in primary accessions (Fig. 1) into a new PREPACT-internal “RNA_editing” feature (Fig. 2). This process simultaneously checked for consistency and more common mistakes (eg, annotation of the wrong DNA strand), which were resolved automatically, and remaining annotation errors (such as obvious mislabeling of editing positions or misannotation of splicing) were corrected manually. Where no editing was annotated at all (eg, most angiosperm chloroplast [cp] DNA entries) RNA editing annotation was introduced manually into the same modifications database.
An auto-annotation module was created to process organelle genome entries without annotated RNA editing sites, but for which complete sets of cDNA are available; for example, the complex mitochondrial (mt) DNAs of lycophytes Isoetes engelmannii and Selaginella moellendorffii for which cDNAs exist as primary database entries, or Vitis vinifera, where editing information has been stored in REDIdb. The auto-annotation script aligns cDNA sequences to the corresponding CDS feature(s) in the organelle genome entries and automatically creates new “RNA_editing” features for these.
Out of a finally-curated organelle genome all CDS features are extracted, translated into proteins taking all corresponding RNA editing into account and stored as a BLAST database, which can be used for analysis. For genomes not being represented by a single accession (eg, the lycophytes mtDNA mentioned above), various accessions can be combined to a single BLAST database.
Lenz H, & Knoop V. (2013). PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. Bioinformatics and Biology Insights, 7, 1-19.
Publication 2013
Chloroplast DNA DNA, Complementary DNA, Mitochondrial Exons Genome Magnoliopsida Organelles Protein Biosynthesis Proteins Selaginella Trees Vitis

Most recents protocols related to «Chloroplast DNA»

1
Soil Microbiome DNA Extraction and Amplification
Total genomic DNA was extracted from each rhizosphere soil or root samples using a Power Soil® DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA) according to the manufacturer’s instructions. To assess DNA concentration and purity, the DNA extracts were run on 1% agarose gels at 110 V for 30 min and quantified using a NanoDrop 2000 spectrophotometer (Thermo Scientific). The extracted total genomic DNA samples were stored at 20 °C until subjected to high-throughput sequencing.
Approximately 400-bp DNA fragments of the bacterial 16S rRNA gene targeting the hypervariable region V3-V4 were amplified using barcoded universal primer pair 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′) in the bacterial community analysis for the five plant species [22 (link)]. To minimize the effect of chloroplast DNA of host plant on microbiota analyses, another barcoded universal primer pair 799F (5′-AACMGGATTAGATACCCKG-3′) and 1193R (5′-ACGTCATCCCCACCTTC C-3′), spanning ~ 450 bp of the V5-V7 regions of the 16S rRNA gene, was used in the subsequent community analysis, including the analysis of tomato microbiota at different developmental stages, and of tomato amended with different nitrogen sources [35 (link), 43 (link), 72 (link)]. Amplified PCR products in each experiment were separately processed to purify, combined in equimolar ratios, and subjected to high-throughput sequencing on an Illumina Mi-Seq sequencing platform, and paired 250-nucleotide reads were produced at Sangon Biotech (Shanghai, China).
Li Y., Lei S., Cheng Z., Jin L., Zhang T., Liang L.M., Cheng L., Zhang Q., Xu X., Lan C., Lu C., Mo M., Zhang K.Q., Xu J, & Tian B. (2023). Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants. Microbiome, 11, 48.
Full text: Click here
Publication 2023
Bacteria Chloroplast DNA Chloroplasts DNA, Plant Gels Genes, Bacterial Genome isolation Lycopersicon esculentum Microbial Community Nitrogen Nucleotides Oligonucleotide Primers Plant Roots Plants Rhizosphere Ribosomal RNA Genes RNA, Ribosomal, 16S Sepharose
2
DNA Extraction and PCR Identification
ADNVs were collected and their genomic DNA was isolated using DNeasy Blood & Tissue Kits (Qiagen, 69504). DNA in the nuclear, chloroplast and mitochondria was identified by PCR (Takara, R010A) following the manufacturer’s instructions. The primer used for target genes were shown in Additional file 1: Table S2. The products were separated by electrophoresis on a 1% agarose gel stained with ethidium bromide (EB).
Liu J., Xiang J., Jin C., Ye L., Wang L., Gao Y., Lv N., Zhang J., You F., Qiao H, & Shi L. (2023). Medicinal plant-derived mtDNA via nanovesicles induces the cGAS-STING pathway to remold tumor-associated macrophages for tumor regression. Journal of Nanobiotechnology, 21, 78.
Full text: Click here
Publication 2023
BLOOD Chloroplast DNA Electrophoresis Ethidium Bromide Genes Genome Mitochondria Oligonucleotide Primers Sepharose Tissues
3
Chloroplast RNA Extraction from Tobacco
Chloroplasts were extracted according to “Extraction of Chloroplast Proteins from Transiently Transformed Nicotiana benthamiana Leaves” bio protocol (Klinkenberg 2014 (link); Klinkenberg et al. 2014 (link)). Briefly, fresh leaf tissue was ground, filtered and centrifuged through a Percoll gradient and visualized on an inverted microscope. Chloroplasts were then shock-frozen and total RNA was isolated from purified chloroplasts using Trizol (Thermo Fisher Scientific, Waltham, MA) or RNeasy Plant Mini kit (Qiagen, Germantown, MD) as per manufacturers’ instructions. For each plant, approximately 100 mg of tissue was ground from each leaf to isolate chloroplast RNA. Leaves from individual plants were pooled. Removal of chloroplast DNA was done by treating the samples with Ambion rDNase1 (Thermo Fisher Scientific, Waltham, MA). Because rRNA typically constitutes over 75% of total RNA and its depletion can results in very low yields of RNA for cDNA preparation, rRNA depletion was not performed. The RNA integrity of the isolated RNA was examined on a Bioanalyzer machine and quantitated on a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) prior to library preparation. For cDNA synthesis, about one microgram of non rRNA-depleted RNA was used to make double strand cDNA (ds-cDNA) and dsDNA was produced using the Invitrogen SuperScript II Double Stranded cDNA Synthesis kit (Thermo Fisher Scientific, Waltham, MA) with random hexamers primers for first-strand synthesis. The cleaned ds-cDNA was then used to construct a library using the Illumina Next Tera Library prep kit with no adaptations (Illumina, Inc, San Diego, CA). After examination of the library quality using the Bioanalyzer (Agilent, Santa Clara, CA), multiplexed libraries were sequenced using the Illumina MiSeq sequencing platform per standard MiSeq run parameters (Illumina protocol manuals).
McCray T.N., Azim M.F, & Burch-Smith T.M. (2023). The dicot homolog of maize PPR103 carries a C-terminal DYW domain and is required for C-to-U editing of chloroplast RNA transcripts. Research Square.
Full text: Click here
Publication Preprint 2023
Acclimatization Anabolism cDNA Library Chloroplast DNA Chloroplast Proteins Chloroplasts DNA, Complementary DNA, Double-Stranded Freezing Microscopy Nicotiana Oligonucleotide Primers Percoll Plant Leaves Plants Ribosomal RNA RNA, Chloroplast Shock Tissues trizol
4
Identification of Intronless Genes in Poaceae
The IGs in the nine species were obtained using the General Feature Format Version 3 (GFF3) file. First, genes that contain the line “CDS” were extracted from the GFF3 file. Redundant sequences representing the same loci were excluded. Genes containing only one line for “exon” were extracted from each genome and used as candidate sequences for further analyses. If there was only one line for “exons,” the coding sequence was considered to lack introns and the gene was designated as intronless. Because mitochondrial and chloroplast DNA do not contain introns, genes labeled “MT” and “PT” were deleted. Genes that were not mapped to chromosomes were also eliminated. To ensure that IGs were accurately identified, all candidate genes were verified using the SMART online tool (http://smart.embl-heidelberg.de). Finally, a non-redundant IG data set for nine Poaceae species was generated. After excluding the IGs, the remaining genes were considered to be potential MEGs. The longest coding sequences were selected as the representative transcripts to generate MEG data sets for the subsequent analyses. The number of introns in each coding gene was extracted from the GFF3 file using the Python script (https://github.com/irusri/Extract-intron-from-gff3).
Chen Y., Ma T., Zhang T, & Ma L. (2023). Trends in the evolution of intronless genes in Poaceae. Frontiers in Plant Science, 14, 1065631.
Full text: Click here
Publication 2023
Chloroplast DNA Chromosomes Exons Genes Genome Introns Mitochondrial Inheritance Open Reading Frames Poaceae Python Sequence Analysis
5
Phylogenetic Analysis of Cenchrinae Grasses
The aligned data matrix used in the phylogenetic analyses includes a total of 180 accessions, of which 172 are ingroup corresponding to 22 (of 24) genera of the subtribe Cenchrinae [see Supporting Information Table S1]. The chloroplast DNA (cpDNA) ndhF matrix previously published [29 (link)], excluding the outgroup, was completed with 63 new sequences. Of these, we have sequenced 20 new accessions corresponding to species of the subgenera Paurochaetium and Reverchoniae of Setaria (Table S1, indicated with *) including those without a defined placement in [29 (link)] (Table S1, indicated with **) plus a second accession of Alexfloydia repens and Panicum antidotale. Eight species belonging to six closely related genera were selected as outgroup, based on [1 (link),29 (link)]: Aakia (Paspaleae, Paspalinae), Eriochloa Kunth, Moorochloa Veldkamp, Rupichloa Salariato & Morrone, Urochloa P. Beauv. (Paniceae, Melinidinae) and Panicum (Paniceae, Panicinae). Information about vouchers and accession numbers of the new sequences obtained for this study and those available in GenBank are given in Table S1.
Delfini C., Aliscioni S.S., Acosta J.M., Pensiero J.F, & Zuloaga F.O. (2023). An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L.. Plants, 12(4), 749.
Full text: Click here
Publication 2023
Chloroplast DNA Panicum Panicum miliare Setaria Plants

Top products related to «Chloroplast DNA»

1
Dneasy plant mini kit by Qiagen
Sourced in Germany, United States, United Kingdom, Canada, China, Spain, Netherlands, Japan, France, Italy, Switzerland, Australia, Sweden, Portugal, India
The DNeasy Plant Mini Kit is a lab equipment product designed for the isolation and purification of DNA from plant samples. It utilizes a silica-based membrane technology to extract and concentrate DNA effectively from a variety of plant materials.
2
Plant genomic dna kit by Tiangen Biotech
Sourced in China
The Plant Genomic DNA Kit is a laboratory equipment designed for the efficient extraction and purification of high-quality genomic DNA from plant samples. It provides a straightforward and reliable method for obtaining DNA suitable for downstream applications such as PCR, sequencing, and analysis.
3
Nanodrop 2000 by Thermo Fisher Scientific
Sourced in United States, China, Germany, Japan, United Kingdom, Spain, Canada, France, Australia, Italy, Switzerland, Sweden, Denmark, Lithuania, Belgium, Netherlands, Uruguay, Morocco, India, Czechia, Portugal, Poland, Ireland, Gabon, Finland, Panama
The NanoDrop 2000 is a spectrophotometer designed for the analysis of small volume samples. It enables rapid and accurate quantification of proteins, DNA, and RNA by measuring the absorbance of the sample. The NanoDrop 2000 utilizes a patented sample retention system that requires only 1-2 microliters of sample for each measurement.
4
Hiseq 2500 by Illumina
Sourced in United States, China, Germany, United Kingdom, Canada, Switzerland, Sweden, Japan, Australia, France, India, Hong Kong, Spain, Cameroon, Austria, Denmark, Italy, Singapore, Brazil, Finland, Norway, Netherlands, Belgium, Israel
The HiSeq 2500 is a high-throughput DNA sequencing system designed for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis. The system utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality sequencing data with speed and accuracy.
5
Abi 3130xl genetic analyzer by Thermo Fisher Scientific
Sourced in United States, United Kingdom, Japan, Germany, Canada
The ABI 3130xl Genetic Analyzer is a capillary electrophoresis instrument designed for DNA sequencing and fragment analysis. It employs laser-induced fluorescence detection to analyze DNA samples. The instrument can process multiple samples simultaneously and provides high-resolution data for various genetic applications.
6
Nebnext ultra dna library prep kit by Illumina
Sourced in United States, United Kingdom, Germany, Belgium
The NEBNext Ultra DNA Library Prep Kit is a product designed for the preparation of DNA libraries for next-generation sequencing. The kit provides the necessary reagents and protocols for the enzymatic fragmentation of DNA samples, followed by the ligation of adapter sequences and subsequent PCR amplification. The core function of this kit is to generate sequencing-ready DNA libraries from various input materials, such as genomic DNA or PCR amplicons, in a streamlined and efficient manner.
7
Hiseq x ten by Illumina
Sourced in United States, China, Australia, Japan, Germany, Hong Kong, Sweden, United Kingdom
The HiSeq X Ten is a high-throughput DNA sequencing system manufactured by Illumina. It is designed to deliver large-scale whole-genome sequencing data. The system utilizes Illumina's proprietary sequencing technology to provide rapid and accurate DNA sequencing capabilities.
8
Sequencher v5 by Gene Codes
Sourced in United States, Japan
Sequencher v5.1 is a DNA and RNA sequence assembly software developed by Gene Codes Corporation. It is used to assemble and analyze DNA and RNA sequences from various sources, including Sanger sequencing, next-generation sequencing, and other sequencing technologies. The software provides tools for sequence editing, alignment, and contig assembly.
9
Nd 2000 spectrometer by Thermo Fisher Scientific
Sourced in United States
The ND-2000 spectrometer is a compact, high-performance instrument designed for spectroscopic analysis. It features a broad wavelength range, high resolution, and a robust design. The ND-2000 is capable of performing a variety of spectroscopic measurements, including absorption, fluorescence, and reflectance.
10
Nanodrop 2000 spectrophotometer by Thermo Fisher Scientific
Sourced in United States, Germany, China, United Kingdom, Japan, Canada, France, Italy, Australia, Spain, Denmark, Switzerland, Singapore, Poland, Ireland, Belgium, Netherlands, Lithuania, Austria, Brazil
The NanoDrop 2000 spectrophotometer is an instrument designed to measure the concentration and purity of a wide range of biomolecular samples, including nucleic acids and proteins. It utilizes a unique sample retention system that requires only 1-2 microliters of sample to perform the analysis.

More about "Chloroplast DNA"

Chloroplast DNA (cpDNA) refers to the genetic material found within the chloroplasts of plant and algal cells.
Chloroplasts are organelles responsible for photosynthesis and contain their own circular DNA molecules, distinct from the nuclear genome. cpDNA is maternally inherited, haploid, and contains genes related to photosynthesis, metabolism, and other essential chloroplast functions.
Analyzing cpDNA can provide valuable insights into plant evolution, phylogenetics, and genetic diversity.
Researchers can optimize their cpDNA analysis using PubCompare.ai, an AI-driven research protocol platform that helps locate the best methods from literature, preprints, and patents.
This streamlines the research process and helps scientists find the most effective techniques for their chloroplast DNA projects.
The DNeasy Plant Mini Kit and Plant Genomic DNA Kit are commonly used for extracting high-quality cpDNA from plant samples.
The NanoDrop 2000 and ND-2000 spectrometers can be used to assess the quantity and purity of the extracted cpDNA.
Next-generation sequencing platforms like the HiSeq 2500, HiSeq X Ten, and ABI 3130xl Genetic Analyzer can be employed for cpDNA sequencing, while the NEBNext Ultra DNA Library Prep Kit can be utilized for library preparation.
The Sequencher v5.1 software can assist with the analysis and assembly of cpDNA sequences.
Experrience the power of AI-driven protocol selection with PubCompare.ai and streamline your chloroplast DNA research.