Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes.

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Publisher: Elsevier B.V.
Document Type: Report
Length: 425 words

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Keywords Koenigia delicatula; Plastome structure; ndh gene loss; Mitochondrial genes; Phylogenetics; Evolutionary rate variation Highlights * Plastomes and mitochondrial genes from 13 Koenigia species were assembled. * Highly-supported conflicting relationships between plastome and mitochondrial trees complicates circumscription of Koenigia. * Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia. * The plastome of Koenigia delicatula is reduced and all ndh genes were lost or pseudogenized. Abstract Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species. Most Persicarieae plastomes exhibit a conserved structure and content relative to other flowering plants. However, Koenigia delicatula has lost functional copies of all ndh genes and the intron from atpF. In addition, the rpl32 gene was relocated in the K. delicatula plastome, which likely occurred via overlapping inversions or differential expansion and contraction of the inverted repeat. The highly supported but conflicting relationships between plastome and mitochondrial trees and among gene trees complicates the circumscription of Koenigia, which could be caused by rapid diversification within a short period. Moreover, the plastome and mitochondrial trees revealed correlated variation in substitution rates among Persicarieae species, suggesting a shared underlying mechanism promoting evolutionary rate variation in both organellar genomes. The divergence of dwarf K. delicatula from other Koenigia species may be associated with the well-known Eocene Thermal Maximum 2 or Early Eocene Climatic Optimum event, while diversification of the core-Koenigia clade associates with the Mid-Miocene Climatic Optimum and the uplift of Qinghai-Tibetan Plateau and adjacent areas. Author Affiliation: (a) Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China (b) Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA (c) Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA * Corresponding authors at: Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA (J.P. Mower). Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China (Shou-Jin Fan). Article History: Received 20 July 2021; Revised 19 January 2022; Accepted 1 June 2022 (footnote)1 Co-first author. Byline: Xiao-Jian Qu (a,1), Xue-Jie Zhang (a,1), Dong-Ling Cao (a), Xiu-Xiu Guo (a), Jeffrey P. Mower [jpmower@unl.edu] (b,c,*), Shou-Jin Fan [fansj@sdnu.edu.cn] (a,*)

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Gale Document Number: GALE|A708782308