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

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.

The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales

“…Repetitive sequences are substrates for recombination and cp genome rearrangements (Milligan et al, 1989), and the number and distribution of these sequences vary from one species to another. For instance, the cp genome of J. curcas contains 72 repetitive sequences that are distributed in intergenic regions, introns and coding sequences (Asif et al, 2010), whereas in V. vinifera , 36 repetitive sequences were found, one in the coding regions of the psaA and psaB genes (Jansen et al, 2006), as in P. edulis , but 58% were palindromes and 12 exist in the ycf2 gene.…”

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

“…The availability of this data provides new insight into the chloroplast genomics, phylogenetic studies, rearrangement of genomes, sequence divergence, simple sequence repeats analysis, and the study of nucleotide substitution in these genomes. Euphorbiaceae is a large family and the number of the sequenced chloroplast genome is very limited [29]. The two sequenced cp genomes are comparatively analyzed with another cp genome to study the various parameters of these genomes.…”

Identification of Suitable Reference Genes for Gene Expression Normalization in Jatropha curcas L During Development and Under Stress Conditions Using Real Time Quantitative PCR

“…For instance, details about the enzymatic pathways of the biosynthesis of lipids and of toxic phorbol esters (PE), as well as, related genes when these seeds are exposed to different types of stress (Rocha et al 2013). Recent release of the complete nuclear and chloroplast genomes (Sato et al 2011;Asif et al 2010) of this species, as well Biological Applied Sciences Braz. Arch.…”