@article{b9a92cb357184646aafe2fcf22aaa4ab,
title = "The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes",
abstract = "The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.",
keywords = "IRLC, Leguminosae, plastid genome, recombination, repeat accumulation, ycf",
author = "Chaehee Lee and Choi, {In Su} and Domingos Cardoso and {de Lima}, {Haroldo C.} and {de Queiroz}, {Luciano P.} and Wojciechowski, {Martin F.} and Jansen, {Robert K.} and Ruhlman, {Tracey A.}",
note = "Funding Information: This work was supported by grants from the National Science Foundation (DEB‐1853024) to RKJ, TAR and MFW, the Texas Ecological Laboratory (EcoLab) to RKJ, TAR and IC, the Sidney F. and Doris Blake Professorship in Systematic Botany to RKJ, the CNPq (Research Productivity Fellowship no. 308244/2018‐4; Universal no. 422325/2018‐0) and FAPESB (Universal no. APP0037/2016) to DC. The authors thank the TEX‐LL, HUEFS, and RB herbaria for voucher deposition, the Desert Legume Program for seeds and Alessandra Schnadelbach and Hedina Basile for their support at UFBA. The authors thank Luciano Paganucci de Queiroz (UEFS) and George Yatskievych (TEX/LL) for arranging a formal Material Transfer Agreement (Decree number 8772) to facilitate research activities between the institutions. The authors thank two anonymous reviewers for their valuable comments. All authors confirm no conflict of interest. Funding Information: This work was supported by grants from the National Science Foundation (DEB-1853024) to RKJ, TAR and MFW, the Texas Ecological Laboratory (EcoLab) to RKJ, TAR and IC, the Sidney F. and Doris Blake Professorship in Systematic Botany to RKJ, the CNPq (Research Productivity Fellowship no. 308244/2018-4; Universal no. 422325/2018-0) and FAPESB (Universal no. APP0037/2016) to DC. The authors thank the TEX-LL, HUEFS, and RB herbaria for voucher deposition, the Desert Legume Program for seeds and Alessandra Schnadelbach and Hedina Basile for their support at UFBA. The authors thank Luciano Paganucci de Queiroz (UEFS) and George Yatskievych (TEX/LL) for arranging a formal Material Transfer Agreement (Decree number 8772) to facilitate research activities between the institutions. The authors thank two anonymous reviewers for their valuable comments. All authors confirm no conflict of interest. Publisher Copyright: {\textcopyright} 2021 Society for Experimental Biology and John Wiley & Sons Ltd",
year = "2021",
month = aug,
doi = "10.1111/tpj.15351",
language = "English (US)",
volume = "107",
pages = "861--875",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "3",
}