Journal of Molecular Evolution

, Volume 84, Issue 4, pp 187–203 | Cite as

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

  • Erika N. Schwarz
  • Tracey A. Ruhlman
  • Mao-Lun Weng
  • Mohammad A. Khiyami
  • Jamal S. M. Sabir
  • Nahid H. Hajarah
  • Njud S. Alharbi
  • Samar O. Rabah
  • Robert K. Jansen
Original Article


This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids. Unsurprisingly, this pattern was significantly correlated with growth habit as most papilionoids are herbaceous, whereas caesalpinioids and mimosoids are largely woody. Both nonsynonymous (dN) and synonymous (dS) substitution rates were also correlated with several biological features including plastome size and plastomic rearrangements such as the number of inversions and indels. In agreement with previous reports, we found that genes in the IR exhibit between three and fourfold reductions in the substitution rates relative to genes within the large single-copy or small single-copy regions. Furthermore, former IR genes in IR-lacking taxa exhibit accelerated rates compared with genes contained in the IR.


Plastomes Inverted repeat Genomic rearrangements Fabaceae Generation time 



The authors gratefully acknowledge the financial support from the President of King Abdulaziz University (KAU) Jeddah, Saudi Arabia, Prof. Dr. Abdulrahman O. Alyoubi. The authors also thank the Genome Sequencing and Analysis Facility at the University of Texas at Austin for performing the Illumina sequencing; the Texas Advanced Computing Center at the University of Texas at Austin for access to supercomputers; TEX-LL for serving as a repository for voucher specimens; and four anonymous reviewers for their valuable suggestions on an earlier version of the manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Erika N. Schwarz
    • 1
    • 2
  • Tracey A. Ruhlman
    • 2
  • Mao-Lun Weng
    • 2
    • 3
  • Mohammad A. Khiyami
    • 4
  • Jamal S. M. Sabir
    • 5
  • Nahid H. Hajarah
    • 5
  • Njud S. Alharbi
    • 5
  • Samar O. Rabah
    • 6
  • Robert K. Jansen
    • 2
    • 5
  1. 1.Department of Biological SciencesSt. Edward’s UniversityAustinUSA
  2. 2.Department of Integrative BiologyUniversity of Texas at AustinAustinUSA
  3. 3.Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsUSA
  4. 4.King Abdulaziz City for Science and Technology (KACST)RiyadhSaudi Arabia
  5. 5.Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of ScienceKing Abdulaziz UniversityJeddahSaudi Arabia
  6. 6.Department of Biological Sciences, Faculty of ScienceKing Abdulaziz UniversityJeddahSaudi Arabia

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