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Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa Sect

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Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa Sect G C A T T A C G G C A T genes Article Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae) Ji-Hyeon Jeon and Seung-Chul Kim * Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-31-299-4499 Received: 4 November 2018; Accepted: 27 December 2018; Published: 3 January 2019 Abstract: Species belonging to Rosa section Synstylae (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section Synstylae have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section Synstylae, Rosa multiflora, Rosa luciae and Rosa maximowicziana are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section Synstylae, and to compare with other infrageneric groups. We found that three Rosa sect. Synstylae species had lost infA genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions (ndhF and ycf1) and five non-coding regions (5’matK-trnK, psbI-trnS-trnG, rps16-trnG, rpoB-trnC, and rps4-trnT) were identified as being highly informative markers. Within three section Synstylae chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of R. multiflora, R. luciae and R. maximowicziana could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of Rosa sect. Synstylae, and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies. Keywords: Rosaceae; Rosa; section Synstylae; Rosa multiflora; Rosa luciae; Rosa maximowicziana; chloroplast genome; genome comparison 1. Introduction The genus Rosa L. (Rosaceae) comprises approximately 125–200 species, distributed through the temperate and subtropical regions of the Northern hemisphere [1–3]. In the conventional taxonomy, genus Rosa is divided into four subgenera (Hulthemia, Rosa, Platyrhodon, and Hesperhodos), and the subgenus Rosa is further divided into 10 sections (Pimpinellifoliae, Gallicanae, Caninae, Carolinae, Rosa, Synstylae, Chinenses [syn. Indicae], Banksianae, Laevigatae, and Bracteatae)[1,4,5]. The Rosa section Synstylae DC. comprises approximately 36 species, which are well-circumscribed with the distinctive synapomorphic characteristic of connate styles into an exserted column [1,5], while the phylogenetic consectionality with section Chinenses has been suggested, from several previous studies [2,5–8]. Rosa sect. Synstylae species are mostly distributed in East Asia, of which Rosa multiflora Thunb. and Rosa luciae Franch. & Rochebr. ex Crép (syn. Rosa wichurana Crép) are the most well-known species, as ones of the wild ancestors of cultivated roses [9]. Rosa sect. Synstylae species are known to be recently diverged, based on poor resolutions and low support values from many previous molecular phylogenetic studies [2,6–8,10,11]. Even the most recent attempt to reconstruct the phylogeny of section Genes 2019, 10, 23; doi:10.3390/genes10010023 www.mdpi.com/journal/genes Genes 2019, 10, x FOR PEER REVIEW 2 of 14 Genes 2019, 10, 23 2 of 14 such as species delimitation failure, poor resolutions, and low support values, and inconsistency Synstylaeamong genedid trees not resolve[5]. Another the phylogenetic evidence support relationshipsing the close with species several relationships phylogenetic in problems, section Synstylae such as speciesis incomplete delimitation reproductive failure, poorbarriers resolutions, among andcongeneric low support species values, [12,13]. and inconsistencyIndeed, the phylogenetic among gene treesreconstruction [5]. Another of genus evidence Rosa supporting has been notoriously the close species difficult, relationships due to low in sequence section Synstylae divergenceis incomplete level and reproductivehybridization barriers[7]. among congeneric species [12,13]. Indeed, the phylogenetic reconstruction of genusChloroplastsRosa has been are notoriously the photosynthetic difficult, due organelles to low sequence in plant divergence cells, and levelthe chloroplast and hybridization genomes [7]. containChloroplasts various essential are the photosynthetic genes for carbon organelles fixati inon plant and cells,metabolite and the synthesis. chloroplast Most genomes chloroplast contain variousgenomes essential range from genes 120 for to carbon170 kb fixationin size, and and have metabolite the quadripartite synthesis. Moststructure, chloroplast in which genomes two inverted range fromrepeats 120 (IRs) to 170 are kb separated in size, and by havea large the single-copy quadripartite region structure, (LSC) in and which a small two single-copy inverted repeats region (IRs) (SSC) are separated[14]. Their bygenomic a large structure, single-copy gene region content, (LSC) gene and or a smallder, and single-copy base composition region (SSC) are known [14]. Their to be genomic highly structure,conserved, gene especially content, in gene IR order,regions. and For base decades, composition various are knownchloroplast to be genome highly conserved, regions have especially been inidentified IR regions. as useful For decades, molecular various markers chloroplast in systematic genome and regions population have been genetic identified studies as useful [15,16]. molecular Whole- markerschloroplast in systematicgenome sequencing, and population with genetic the advent studies of [15high-throughput,16]. Whole-chloroplast next-generation genome sequencing,sequencing withtechnique, the advent now generates of high-throughput massive sequence next-generation data, helping sequencing to overcome technique, the nowpreviously generates unresolved massive sequencerelationships. data, It helping also provides to overcome genomic the previously information unresolved (e.g., relationships.structure, gene It alsoorder, provides and content), genomic informationmutations in (e.g.,which structure, imply the gene presence order, of and the content), critical events mutations in the in evolutionary which imply histories. the presence of the criticalIn eventsthe Eastern in the Sino-Japanese evolutionary histories.floristic region, Chang et al. [17] suggested three major florae: the AmurIn theflora, Eastern the Sino-JapaneseLiaoning–Shand floristicong region,flora, Changand the et al.Southern [17] suggested Chinese–Japanese three major florae: flora. the Three Amur flora,representative the Liaoning–Shandong species of Rosa flora, sect. and Synstylae the Southern in this Chinese–Japanese study, i.e., R. flora. multiflora Three, representative R. luciae, and species Rosa ofmaximowiczianaRosa sect. Synstylae Regel,in are this widely study, i.e.,distributedR. multiflora in the, R. East luciaeern, and Sino-JapaneseRosa maximowicziana floristic region,Regel, are and widely each distributedspecies represents in the Eastern different Sino-Japanese floristic elements. floristic Rosa region, multiflora and each is speciesfound representsin the Liaoning–Shandong different floristic elements.flora, whileRosa R. multifloraluciae andis R. found maximowicziana in the Liaoning–Shandong occur in the Southern flora, while ChineseR. luciae floraand andR. the maximowicziana Amur flora, occurrespectively in the Southern (Figure Chinese1). Though flora andtheir the distributi Amur flora,ons respectivelyare to some (Figure extent,1). Though parapatric their distributions(between R. aremaximowicziana to some extent, and parapatric R. multiflora (between/R. luciaeR. maximowicziana) or to overlap anda largeR. multiflora portion /(betweenR. luciae) orR. tomultiflora overlap and a large R. portionluciae), these (between speciesR. multiflora are distinctand R.in luciaethe ecological,), these species morphological, are distinct inor the phenol ecological,ogical morphological,characteristics or(Table phenological 1). While characteristics they have the (Table evident1). Whiledifferences they havein these the evidentcharacteristics, differences their in species these characteristics, relationships theiror delimitations species relationships were not or clear delimitations with molecular were not cleardata within previous molecular studies, data in suggesting previous studies, short suggestingevolutionary short history evolutionary on them history[2,5–7,10,11]. on them [2,5–7,10,11]. Figure 1. TheThe schematic schematic distribution distribution of of three three Rosa sect. Synstylae species. ( (AA)) RosaRosa multiflora multiflora in the Liaoning–Shandong flora; flora; (B) Rosa(B) luciaeRosa inluciae the Southern in the Chinese–JapaneseSouthern Chinese–Japanese flora; (C) Rosa maximowiczianaflora; (C) Rosain themaximowicziana Amur flora. CN:in the China; Amur KP: flora. Korean CN: Peninsula; China; KP: PK: Korean Primorsky Peninsula; Krai, Russia; PK: Primorsky JA: Japanese Krai, Archipelago. Russia; JA: Japanese Archipelago. Table 1. The ecological, morphological, and phenological characteristics of three species of Rosa sect. Synstylae. InCharacteristics previous studies, onlyRosa several multiflora chloroplast region Rosa data luciae were used to Rosa infer maximowicziana the phylogeny of Rosa sect.Habitat Synstylae
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