The complete chloroplast genome of Populus rotundifolia (Salicaceae)

Zheng, Honglei; Fan, Liqiang; Wang, Tianjing; Zhang, Lei; Ma, Tao; Mao, Kangshan

doi:10.1007/s12686-016-0568-1

Cited by 9 publications

(13 citation statements)

References 7 publications

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“…Although the plastid genome generally has a nearly collinear gene order, changes in the genome, such as sequence inversion and gene expansion or contraction at the boundary of the SC and IR regions, occur over the course of evolution (Cho et al, 2015; Choi et al, 2016). Our results showed that the genome size, gene order, and compositions of the 24 newly sequenced Populus genomes were very similar with each other and with previously sequenced Populus plastid genomes; the genome sizes ranged from 155,177 to 157,839 bp (Chen et al, 2016; Wang et al, 2016; Zheng et al, 2016; Han et al, 2017). Among the genomes, three plastomes of P. alba, P. tomentosa , and P. tomentosa (NC), two plastomes of P. haoana and P. kangdingensis , two plastomes of P. trinervis and P. xiangchengensis , and two plastomes of P. deltoides and P. deltoides × nigra , each had the same length.…”

Section: Discussionsupporting

confidence: 78%

“…To estimate phylogenetic relationships within the Populus , 59 taxa with available complete plastid genomes and one taxa ( Chosenia arbutifolia ) with seven combined chloroplast fragments [ matK (GenBank accession number: EU790701), ndhF (GenBank accession number: AY757181), rbcL - atpB (GenBank accession number: FJ788535), trnL (GenBank accession number: GQ244791), trnD-trnT (GenBank accession number: FJ788620), rbcL (GenBank accession number: AB012776), and trnL-F (GenBank accession number: AY757062)] were compared, with 40 taxa from Populus , fifteen taxa from Salix and four taxa from four genera that are members of the Salicaceae family, Flacourtia indica (GenBank accession number: MG262341), Idesia polycarpa (GenBank accession number: KX229742), Itoa orientalis (GenBank accession number: MG262342), and Poliothyrsis sinensis (GenBank accession number: MG262343) were sampled as outgroups. The 40 Populus genomes comprised the 24 new plastomes and sixteen previously published complete plastomes adopted from the NCBI (Chen et al, 2016; Wang et al, 2016; Zheng et al, 2016; Zong et al, 2019). The complete genome matrix was aligned using MAFFT version 7 software (Katoh and Standley, 2013) and then manually edited using MEGA 5 (Tamura et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

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Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

et al. 2019

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Populus, a core genus of Salicaceae, plays a significant ecological role as a source of pioneer species in boreal forests. However, interspecific hybridization and high levels of morphological variation among poplars have resulted in great difficulty in classifying species for systematic and comparative evolutionary studies. Here, we present phylogenetic analyses of 24 newly sequenced Populus plastomes and 36 plastomes from GenBank, which represent seven genera of Salicaceae, in combination with a matrix of eighteen morphological characters of 40 Populus taxa to reconstruct highly supported relationships of genus Populus. Relationships among the 60 taxa of Salicaceae strongly supported two monophyletic genera: Populus and Salix. Chosenia was nested within the genus Salix, and five clades within Populus were divided. Clade I included the three taxa P. euphratica, P. pruinosa, and P. ilicifolia. Clade II contained thirteen taxa [P. adenopoda, P. alba, P. bolleana, P. davidiana, P. hopeiensis, P. nigra, P. qiongdaoensis, P. rotundifolia, P. rotundifolia var. duclouxiana, P. tremula, P. tremula × alba, P. tomentosa, and P. tomentosa (NC)]. Clade III included the ten taxa P. haoana, P. kangdingensis, P. lasiocarpa, P. pseudoglauca, P. qamdoensis, P. schneideri, P. simonii, P. szechuanica, P. szechuanica var. tibetica, and P. yunnanensis. Clade IV included P. cathayana, P. gonggaensis, P. koreana, P. laurifolia, P. trinervis, P. wilsonii, and P. xiangchengensis. The last clade comprised P. angustifolia, P. balsamifera, P. deltoides, P. deltoides × nigra, P. fremontii, P. mexicana, and P. trichocarpa. This phylogeny is also supported by morphological traits, including bark smoothness, bud size, petiole shape, leaf inflorescence, male anther length and male anther tip.

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Section: Discussionsupporting

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

et al. 2019

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“…Primers for the ndh C- trn V fragment were designed according to the complete chloroplast genomes of P. rotundifolia (GenBank accession number KX425853; Zheng et al, 2016) and P. alba (GenBank accession number AP008956; Okumura et al, 2006; Table S3B). Primers for the other cpDNA fragments were taken from Feng et al (2013) (Table S3B).…”

Section: Methodsmentioning

confidence: 99%

Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China

et al. 2017

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Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.

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“…Besides, Shao and Xu (2015) studied the development and function of the strumae of O. hainanense, which was found to provide flower visitors a nutritious and safe place for mating, oviposition, brooding and perhaps some food such as polysaccharides. Complete chloroplast sequences can provide insights into the evolutionary history and natural selection process for many plants (Inoue 2011;Zheng et al 2016). In this study, we reported and characterized the complete chloroplast genome sequence of O. hainanense to contribute to further phylogenetical and protective studies of this plant.…”

Section: Oncodostigma Hainanense; Endangered Species; Chloroplast Genmentioning

confidence: 99%

The complete chloroplast genome sequence of an endangered species, Oncodostigma hainanense

Zhang

et al. 2019

Mitochondrial DNA Part B

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2019) The complete chloroplast genome sequence of an endangered species, Oncodostigmahainanense, Mitochondrial DNA Part B, 4:1, 721-722, ABSTRACTOncodostigma hainanense is an endangered species with extremely small populations due to human activities in China. This study presents the chloroplast genome of the plant by de novo assembly using the whole-genome sequencing data. The size of the complete chloroplast genome was 160,497 bp in length, comprising a large single copy region (LSC) of 89,424 bp, a small single copy region (SSC) 18,948 bp, and inverted repeat regions (IRS) of 26,061 bp. A total of 135 genes, including 85 proteincoding genes, 42 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 17 genes occur in IRS, containing six protein-coding genes, seven tRNA genes and four rRNA genes. The GC content of O. hainanense was 35.59%. Phylogenetic analysis with seven other species revealed that O. hainanense was clustered with Annona cherimola. ARTICLE HISTORY

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The complete chloroplast genome of Populus rotundifolia (Salicaceae)

Cited by 9 publications

References 7 publications

Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China

The complete chloroplast genome sequence of an endangered species, Oncodostigma hainanense

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