J Syst Evol ›› 2015, Vol. 53 ›› Issue (5): 458-468.DOI: 10.1111/jse.12179

• Research Articles • Previous Articles     Next Articles

Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

Erika N. Schwarz1*, Tracey A. Ruhlman1, Jamal S. M. Sabir2, Nahid H. Hajrah2, Njud S. Alharbi2, Abdulrahman L. Al-Malki3, C. Donovan Bailey4, and Robert K. Jansen1,2   

  1. 1Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
    2Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
    3Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
    4Department of Biology, New Mexico State University, Las Cruces, NM, USA
  • Received:2015-06-26 Published:2015-09-22

Abstract: To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.

Key words: chloroplast genome, Fabaceae, genomic rearrangement, legumes, parallel inversions, rps16