The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

Anna V. Williams, Laura M. Boykin, Katharine A. Howell, Paul G. Nevill, Ian Small, Chih-Horng Kuo
2015 PLoS ONE  
Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp
more » ... d 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex. Results and Discussion Sequencing and assembly Dried herbarium material of a specimen of Acacia ligulata Benth. was used for DNA extraction. Illumina sequencing of a library prepared from total DNA produced 2,216,882 paired-end reads with a read length of 100 nt. 5.26% of reads were assembled into 23 contigs showing homology to legume plastid DNA. Gaps between contigs were then filled by PCR amplification and Sanger sequencing. The complete assembled chloroplast genome of A. ligulata is typical in its general structure with a pair of IRs of 25,925 bp, an LSC of 88,576 bp and an SSC of 18,298 bp (Fig 1) . Thus, unlike the chloroplast genomes of many of the Papilionoideae, the A. ligulata Acacia ligulata Chloroplast Genome PLOS ONE |
doi:10.1371/journal.pone.0125768 pmid:25955637 pmcid:PMC4425659 fatcat:micerd5bp5dpxo6ehvufzm5ndy