DNA Extraction for plant samples by CTAB v1

Yang, Ting

doi:10.17504/protocols.io.pzqdp5w

Cited by 4 publications

(5 citation statements)

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“…We have optimized the DNA extraction protocol and published it via the protocols.io platform [20]. We will soon launch a DNA extraction kit for high-molecular-weight genomic DNA that is suitable for 10X Genomic analysis [16]. We also have just finished writing a guideline on sample submission for 10KP, which includes sample preparation (fresh sample, DNA sample, and RNA sample), sample packing, and shipping.…”

Section: Discussionmentioning

confidence: 99%

“…All specimens are stored in the CNGB herbarium, and voucher information can be found in Supplementary Table S1 (Additional files). Collected young leaves were shipped to Shenzhen, China, on dry ice, and, using the CTAB method [16], good-quality DNA was extracted from 761 samples.…”

Section: Data Descriptionmentioning

confidence: 99%

“…The data reported in this study are also available in the CNGB Nucleotide Sequence Archive under accession number CNPhis0000538. DNA extraction [16] and BGISEQ-500 whole-genome sequencing library construction protocols can be found via protocols.io [17]. A total of 738 chloroplast genomes and 17 assembled genomes together with raw data supporting the results presented here are available via the GigaScience GigaDB repository and will be continuously updated and linked to the GigaDB entries as new assemblies are completed [40].…”

Section: Availability Of Supporting Datamentioning

confidence: 99%

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Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

Liu¹,

Wei

Yang³

et al. 2019

GigaScience

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Background Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank. Results The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications. Conclusions The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for “planetary-scale” projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.

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Section: Discussionmentioning

confidence: 99%

Section: Data Descriptionmentioning

confidence: 99%

Section: Availability Of Supporting Datamentioning

confidence: 99%

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Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

Liu¹,

Wei

Yang³

et al. 2019

GigaScience

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“…Genomic DNA was extracted either from a tree ( F. albida , M. oleifera ) or from nursery plantlets ( V. subtarranea , L. purpureus , S. birrea ) grown at the World AgroForestry Center campus in Kenya using a modified Cetyl TrimethylAmmonium Bromide (CTAB) method [28].…”

Section: Data Descriptionmentioning

confidence: 99%

The draft genomes of five agriculturally important African orphan crops

Chang

Liu²,

Liao³

et al. 2018

GigaScience

123

118

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Background The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. Results Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea , Lablab purpureus , Faidherbia albida , Sclerocarya birrea , and Moringa oleifera . Assembled genomes range in size from 217 to 654 Mb. In V. subterranea , L. purpureus , F. albida , S. birrea , and M. oleifera , we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. Conclusions These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

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“…All sampled species covering more than 30 genera ( Supplementary Table S4 DNA extraction and target enrichment sequencing for bamboos A total of 358 woody bamboo samples were sampled and sequenced in this study ( Supplementary Table S4), as a practical application of target enrichment sequencing and an evaluation of the capture e ciency. Genomic DNA from each sample was extracted using the CTAB method 13 and fragmented to a peak size of 200 bp using a Covaris E220 sonicator (Covaris, Woburn, Massachusetts, USA), followed by the end-repair, addition of base "A", and adapter ligation. DNA fragments of the desired size (200 bp) were selected on an agarose gel and hybridized to the probes for 72 h. The probes captured DNA fragments were recycled by magnetic beads coated with streptavidin, which interacted with the biotin on the probes to wash away the uncaptured DNA fragments.…”

Section: Taxa Samplingmentioning

confidence: 99%

Targeted Enrichment of Novel Chloroplast-Based Probes Reveals a Large-Scale Phylogeny of 412 Bamboos

Wang

Yang

et al. 2020

Preprint

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Background: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution.Results: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics.Conclusions: The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.

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DNA Extraction for plant samples by CTAB v1

Abstract: DNA extractionof −80◦C stored leaves by CTAB.

Cited by 4 publications

References 0 publications

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

The draft genomes of five agriculturally important African orphan crops

Targeted Enrichment of Novel Chloroplast-Based Probes Reveals a Large-Scale Phylogeny of 412 Bamboos

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