Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing1

نویسندگان

  • Shota Sakaguchi
  • Saneyoshi Ueno
  • Yoshihiko Tsumura
  • Hiroaki Setoguchi
  • Motomi Ito
  • Chie Hattori
  • Shogo Nozoe
  • Daiki Takahashi
  • Riku Nakamasu
  • Taishi Sakagami
  • Guillaume Lannuzel
  • Bruno Fogliani
  • Adrien S. Wulff
  • Laurent L’Huillier
  • Yuji Isagi
چکیده

PREMISE OF THE STUDY 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. METHODS 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. RESULTS 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. DISCUSSION 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).

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Comparative bioinformatics analysis of a wild diploid Gossypium with two cultivated allotetraploid species

Background: Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton. G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different ch...

متن کامل

Comparison of Chloroplast DNA Diversity in Some Iranian Apple Genotypes, Commercial Cultivars and Rootstocks

The chloroplastic DNA of 64 accessions of apple (Malus spp.) (54 Iranian genotypes, five commercial cultivars and five rootstocks) were analyzed to reveal their haplotypes by using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. Approximately 4320 bp of the chloroplast genome was analyzed, by using two chloroplast universal primer pairs and two restriction ...

متن کامل

Loss of Chloroplast trnLUAA Intron in Two Species of Hedysarum (Fabaceae): Evolutionary Implications

Previous studies have indicated that in all land plants examined to date, the chloroplast gene trnLUAA isinterrupted by a single group I intron ranging from 250 to over 1400 bp. The parasitic Epifagus virginiana haslost, however, the entire gene. We report that the intron is missing from the chloroplast genome of twoarctic species of the legume genus Hedysarum (H. alpinum, H. ...

متن کامل

A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing1

PREMISE OF THE STUDY We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. METHODS A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing nove...

متن کامل

DNA REPLICATION AND SYNTHESIS OF DNABINDING PROTEINS IN THE CHLOROPLASTS OF A CALLUS CULTURE

Continuous labelling of callus with H-thymidine results in intermittent peaks of H-DNA per chloroplast, showing synchrony of division. The increase in H-DNA could be due to several replication rounds, and the drop to successive plastid divisions without intervening DNA synthesis. The level of DNA-binding proteins in the chloroplast parallels the peaks of plastidal DNA synthesis; such pro...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره 5  شماره 

صفحات  -

تاریخ انتشار 2017