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.
Highlights
The genus Rosa L. (Rosaceae) comprises approximately 125–200 species, distributed through the temperate and subtropical regions of the Northern hemisphere [1,2,3]
Genus Rosa is divided into four subgenera (Hulthemia, Rosa, Platyrhodon, and Hesperhodos), and the subgenus Rosa is further divided into 10 sections
Synstylae species (R. multiflora, R. luciae, and R. maximowicziana) were from 156,405 bp (R. maximowicziana) to 156,519 bp (R. multiflora), and the depth of coverage for chloroplast genome contigs were from 214× (R. multiflora) to 1418×
Summary
The genus Rosa L. (Rosaceae) comprises approximately 125–200 species, distributed through the temperate and subtropical regions of the Northern hemisphere [1,2,3]. Synstylae species are known to be recently diverged, based on poor resolutions and low support values from many previous molecular phylogenetic studies [2,6,7,8,10,11]. Rosa has been notoriously difficult, due to low divergence level and trees [5] Another evidence supporting the close species relationships insequence section Synstylae is incomplete hybridizationbarriers [7]. I.e., R. multiflora, R. luciae, and Rosa maximowicziana Regel, are widely species represents different floristic elements. Synstylae species (R. multiflora, R. luciae, and R. maximowicziana) were sequenced to (1) understand the chloroplast genomic features of Rosa sect. It will be one of the good model study on the chloroplast genome evolution of very recently diverged species, which are geographically, ecologically, morphologically, or phenologically distinct
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