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The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis

Abstract

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.

Abbreviations

cpDNA:

chloroplast DNA

IR:

inverted repeat

JLA:

junction IRA/LSC

JLB:

junction IRB/LSC

JSA:

junction IRA/SSC

JSB:

junction IRB/SSC

LSC:

large single copy

PCR:

polymerase chain reaction

rRNA:

ribosomal RNA

SSC:

small single copy

tRNA:

transport RNA

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Correspondence to Wojciech Pląder.

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Pląder, W., Yukawa, Y., Sugiura, M. et al. The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis. Cell Mol Biol Lett 12, 584–594 (2007). https://doi.org/10.2478/s11658-007-0029-7

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Key words

  • Organelle
  • Gene order