Posted by: shrikantmantri | June 30, 2010

Tree Genetics and Genomes:Complete sequence and organisation of the Jatropha curcas (Euphorbiaceae) chloroplast genome

Original Paper

Complete sequence and organisation of the Jatropha curcas (Euphorbiaceae) chloroplast genome

Mehar H. Asif1, Shrikant S. Mantri1, Ayush Sharma1, Anukool Srivastava1, Ila Trivedi1, Priya Gupta1, Chandra S. Mohanty1, Samir V. Sawant1 and Rakesh TuliContact Information

(1)  Plant Molecular Biology and Genetic Engineering Division, National Botanical Research Institute Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India

Received: 4 August 2009  Revised: 17 April 2010  Accepted: 6 May 2010  Published online: 27 June 2010

Communicated by J. Dean
Abstract  

Jatropha curcas is an important non-edible oil seed tree species and is considered a promising source of biodiesel. The complete nucleotide sequence of J. curcas chloroplast genome (cpDNA) was determined by pyrosequencing and gaps filled by Sanger sequencing. The cpDNA is a circular molecule of 163,856 bp in length and codes for 110 distinct genes (78 protein coding, four rRNA and 28 distinct tRNA). Genome organisation and arrangement are similar to the reported angiosperm chloroplast genome. However, in Jatropha, the infA and the rps16 genes are non-functional. The inverted repeat (IR) boundary is within the rpl2 gene, and the 13 nucleotides at the ends of the two duplicate genes are different. Repeat analysis suggests the presence of 72 repeat regions (>30 bp) apart from the IR; of these, 48 were direct and 24 were palindromic repeats. Phylogenetic analysis of 81 protein coding chloroplast genes from 65 taxa by maximum parsimony, maximum likelihood and minimum evolution analyses at 100 bootstraps provide strong support for the placement of inaperturate crotonoids of which Jatropha is a member as sister to articulated crotonoids of which Manihot is a member.

Electronic supplementary material  The online version of this article (doi:10.1007/s11295-010-0303-0) contains supplementary material, which is available to authorized users.

Keywords   Jatropha curcas  – Chloroplast – Genome – Phylogeny – Pyrosequencing – Euphorbiaceae – Angiosperms

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