title: Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies.
abstract: 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.
authors.affiliation: Department of Biological Sciences, St. Edward's University, Austin, TX, 78704, USA. enschwarz@utexas.edu.|Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA. enschwarz@utexas.edu.
authors.forename: Erika N
authors.initials: EN
authors.lastname: Schwarz
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.|Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.
authors.forename: Mao-Lun
authors.initials: ML
authors.lastname: Weng
authors.affiliation: King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia.
authors.forename: Mohammad A
authors.initials: MA
authors.lastname: Khiyami
authors.affiliation: Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JSM
authors.lastname: Sabir
authors.affiliation: Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Nahid H
authors.initials: NH
authors.lastname: Hajarah
authors.affiliation: Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Njud S
authors.initials: NS
authors.lastname: Alharbi
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Samar O
authors.initials: SO
authors.lastname: Rabah
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.|Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D019143:Evolution, Molecular; D007887:Fabaceae / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D054627:Genome, Plastid / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics; D009154:Mutation; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny
chemical_list: D009711:Nucleotides
keywords: Fabaceae; Generation time; Genomic rearrangements; Inverted repeat; Plastomes