Dataset Information

Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing.

ABSTRACT: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).

SUBMITTER: Sakaguchi S

PROVIDER: S-EPMC5435405 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing.

Sakaguchi Shota S Ueno Saneyoshi S Tsumura Yoshihiko Y Setoguchi Hiroaki H Ito Motomi M Hattori Chie C Nozoe Shogo S Takahashi Daiki D Nakamasu Riku R Sakagami Taishi T Lannuzel Guillaume G Fogliani Bruno B Wulff Adrien S AS L'Huillier Laurent L Isagi Yuji Y

Applications in plant sciences 20170508 5

<h4>Premise of the study</h4>High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms.<h4>Methods</h4>Chloroplasts were enriched using a high-salt isolation buffer without any st ...[more]

PMID: 28529832

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Project description:BackgroundPleural disease is a common clinical condition, and some patients present with a small amount of pleural effusion or no pleural effusion. It is difficult to diagnose such patients in clinical practice. Medical thoracoscopy is the gold standard for the diagnosis of pleural effusion with unknown origin, and guidelines recommend that pneumothorax should be induced in such patients before medical thoracoscopy examination. However, the process of inducing pneumothorax is tedious and has many complications. Our study was conducted to clarify the value of thoracic ultrasound combined with medical thoracoscopy in patients with small amounts or without pleural effusion to simplify the process of medical thoracoscopy examination.MethodsIn this retrospective study, we included patients who were assigned to complete medical thoracoscopy. Successful completion of medical thoracoscopy in patients was regarded as letting the endoscope get into the pleural cavity and completion of the biopsy. Finally, we analyzed the value of preoperative ultrasound in patients without or with small amounts of pleural effusion.ResultsSeventy-two patients were finally included in the study. Among them, 68 patients who underwent ultrasound positioning of the access site successfully completed the examination and four patients failed the examination. Fifty-one cases showed no fluid sonolucent area at the access site, of which 48 cases had pleural sliding signs at the access site, and 47 patients successfully completed the examination; 3 cases without pleural sliding signs at the access site failed to complete thoracoscopy. In 21 cases, the fluid sonolucent area was selected as the access site, and all of them successfully completed thoracoscopy.ConclusionMedical thoracoscopy is one of the methods to confirm the diagnosis in patients with pleural disease with small amounts or without pleural effusion. The application of thoracic ultrasound before medical thoracoscopy can be used for the selection of the access site. It is possible to replace pneumothorax induction before medical thoracoscopy.

Dataset Information

Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing.

Publications

Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing.

Similar Datasets

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