Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family

BMC Genomics

Research Article

Michael J. Moore¹  Linsen Yang²  Aiping Meng³  Hengchang Wang³  Jianqiang Li³  Yanxia Sun³  Kole F. Adelalu⁴  Nan Lin⁴  Shuguang Jian⁵ 

[1] Department of Biology, Oberlin College, Oberlin, OH, USA;Hubei Key Laboratory of Shennongjia Golden Monkey Conservation Biology, Administration of Shennongjia National Park, Shennongjia, Hubei, China;Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China;Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China;University of Chinese Academy of Sciences, Beijing, China;South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China;

关键词: Early-diverging eudicots;    Circaeasteraceae;    Plastome;    Rearrangements;    Gene loss;    Phylogenetic analyses;   

DOI  :  10.1186/s12864-017-3956-3

 received in 2017-04-03, accepted in 2017-07-24,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAmong the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae.ResultsUsing an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae.Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses.ConclusionThe first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales.

【 授权许可】

CC BY   
© The Author(s). 2017