title: Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.
abstract: The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.
authors.affiliation: Department of Biology, New Mexico State University, P.O. Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA.
authors.forename: Diana V
authors.initials: DV
authors.lastname: Dugas
authors.affiliation: Department of Biology, New Mexico State University, P.O. Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA.
authors.forename: David
authors.initials: D
authors.lastname: Hernandez
authors.affiliation: Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
authors.forename: Erik J M
authors.initials: EJ
authors.lastname: Koenen
authors.affiliation: Department of Integrative Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA.
authors.forename: Erika
authors.initials: E
authors.lastname: Schwarz
authors.affiliation: Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY 14456, USA.|Oregon State University, Department Of Plant Biology, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
authors.forename: Shannon
authors.initials: S
authors.lastname: Straub
authors.affiliation: Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
authors.forename: Colin E
authors.initials: CE
authors.lastname: Hughes
authors.affiliation: Department of Integrative Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA.|Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.affiliation: Department of Biology, New Mexico State University, P.O. Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA.
authors.forename: Madhugiri
authors.initials: M
authors.lastname: Nageswara-Rao
authors.affiliation: Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Staats
authors.affiliation: Department of Biology, New Mexico State University, P.O. Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA.
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Trujillo
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Nahid H
authors.initials: NH
authors.lastname: Hajrah
authors.affiliation: Biotechnology Research Group, 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 Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Abdulrahman L
authors.initials: AL
authors.lastname: Al-Malki
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.affiliation: Department of Biology, New Mexico State University, P.O. Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA.
authors.forename: C Donovan
authors.initials: CD
authors.lastname: Bailey
mesh_terms: D005075:Biological Evolution; D002874:Chromosome Mapping; D005091:Exons; D007887:Fabaceae / Q000145:classification / Q000235:genetics*; D017343:Genes, Plant; D059646:Genome Size; D054627:Genome, Plastid; D007438:Introns; D016366:Open Reading Frames; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D012641:Selection, Genetic; D020080:Tandem Repeat Sequences