Project description:Malus toringoides belongs to the subfamily Amygdaloideae of Rosaceae, which is an endemic species in China. It has significant ornamental, economic, and ecological value. Herein, we assembled the complete chloroplast genome of Malus toringoides using the next-generation sequencing technology. The total length of the complete chloroplast genome was 160,093 base pair (bp), consisting of one large single-copy (LSC) region with a sequence length of 88,177 bp, one small single-copy (SSC) region which sequence length is 19,194 bp, and a pair of inverted repeat regions (IRs, 26361 bp). Besides, the complete chloroplast genome contained 128 genes, namely 83 protein-coding genes (PCGs), 37 tRNA genes (tRNA), and 8 rRNAgenes (rRNA), the GC content was 36.6%. The phylogenetic relationship among species in genus Malus is closely related, especially the phylogenetic relationship among Malus angustifolia, Malus prattii, Malus micromalus, Malus prunifolia, Malus baccata, Malus hupehensis and Malus toringoides. Furthermore, phylogenetic relationship of Malus toringoides in Malus was closely related to Malus hupehensis. Our study affords important genetic information for further researches on the related species.
Project description:Malus toringo (Siebold) Siebold ex de Vriese is a worthy species in the genus Malus (family Rosaceae) distributing from North America and Asia, especially in China. In addition to its ornamental value, the medicinal value of its fruits has also been developed to treat food stagnation diseases. Herein, we obtained the complete chloroplast genome of M. toringo using next-generation sequencing technology. The complete chloroplast genome is 160,039 base pair (bp) in length, including a large single copy (LSC) region of 88,142 bp, a small single copy (SSC) region of 19,183 bp, and a pair of inverted repeat regions (IRs, 26,357 bp). And, the overall GC content of the chloroplast genome was 36.6%. Besides, a total of 128 unique genes were found in the chloroplast genome, namely 83 protein-coding genes (PCGs), 37 tRNA genes (tRNA), and eight rRNA genes (rRNA). A maximum-likelihood phylogenetic tree was reconstructed using the full length of chloroplast genome to show the phylogenetic relationships among species in genus Malus. It was concluded that M. toringo was phylogenetically close to M. angustifolia.
Project description:Malus toringoides belongs to the Malus genus (Rosaceae) and is a precious resource among wild plants. In this study, we report the first complete chloroplast (cp) genome sequence of M. toringoides. The whole cp genome contains 126 genes, 83 protein-coding genes, 35 tRNA genes, and eight rRNA genes. A maximum-likelihood phylogenetic tree analysis based on 12 complete chloroplast genomes indicated that M. toringoides clustered closely with Malus hupehensis. Thus, the chloroplast genome can provide valuable genetic information for the protection and exploitation of M. toringoides.
Project description:The Malus kansuensis belongs to the Malus genus of Rosaceae family and it is an important apple rootstock resource native to China. Here, its complete chloroplast genome was sequenced and assembled by high-throughput Illumina sequencing data. The DNA was circular in shape with 160,133 bp length, containing IRA and IRB inverted repeat regions (26,354 bp), large single-copy region (LSC) (88,141 bp), and small single-copy region (SSC)(19,284 bp). In the chloroplast genome, 129 functional genes were predicted, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic tree basically accords with the traditional taxonomy of the order Malus genus of Rosaceae family.
Project description:Malus prattii (Rosaceae) is an endemic species to China. Here, the complete chloroplast genome of M. prattii was obtained by using Illumina pair-end sequencing. The M. prattii complete chloroplast genome was 160,239 bp in length, containing a large single-copy region (LSC) of 88,355 bp and a small single-copy region (SSC) of 19,176 bp, which were separated by a pair of inverted repeat regions (IRs) of 26,354 bp. The chloroplast genome of Malus prattii contained 112 unique functional genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall C + G content of the whole genome was 36.5%. A neighbour-joining phylogenetic analysis suggested a close relationship between M. prattii and M. micromalus.
Project description:Malus halliana is an important ornamental plant resource. Herein, we determined the complete chloroplast (cp) genome sequence of M. halliana using Illumina sequencing data. The whole cp genome is 160,089 bp in size, consisting of a pair of inverted repeats (IR 52,706 bp), a large single-copy region (LSC 88,189 bp), and a small single-copy region (SSC 19,194 bp). The plastid genome contains 129 genes, 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In addition, a maximum-likelihood phylogenetic analysis demonstrated that M. halliana was most closely related to Malus hupehensis. The complete plastome sequence will provide useful genetic information for phylogenetic studies, the resolution of taxonomic discrepancies, and molecular breeding.
Project description:Malus sieboldii belongs to the genus Malus (Rosaceae) and is commonly considered a good rootstock for apple trees. The chloroplast (cp) genome of M. sieboldii was assembled using Illumina HiSeq sequencing. The whole cp genome is 160,168 bp in size, with a typical quadripartite structure consisting of a pair of inverted repeats (IR 52,716 bp), a large single-copy region (LSC 88,267 bp), and a small single-copy region (SSC 19,185 bp). The plastid genome contains 129 genes, 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Bayesian phylogenetic analysis showed that M. sieboldii is most closely related to M. hupehensis. The cp genome will provide more information about the taxonomy and cp evolution of the genus Malus.
Project description:Prunus davidiana is a Chinese wild peach species belonging to the family Rosaceae. In this study, we first assembled the complete chloroplast (cp) genome of P. davidiana by Illumina paired-end reads data, then carried out phylogenetic analysis. The P. davidiana cp genome was 158,055 bp, containing a large single copy region (LSC) of 86,248 bp and a small single copy region (SSC) of 19,047 bp separated by a pair of inverted repeats (IRs) of 26,380 bp. The cp genome contained 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The result of the phylogenetic analysis showed that P. davidiana is closely related to P. mongolica.
Project description:Rubus eucalyptus Focke belong to genus Rubus in the family Rosaceae, the fresh fruits of which can be used for medicine and cosmetic. The plastome of R. eucalyptus is 155,672 bp in length, with one large single copy region of 85,277 bp, one small single copy region of 18,864 bp, and two inverted repeat (IR) regions of 25,748 bp. It contains 130 genes, including 86 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. Phylogenetic tree shows that R. eucalyptus was at the basal of Rosaceae. The published plastome within Rubus provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Rosaceae.
Project description:The complete chloroplast genome of Rosa laevigata has been characterized by reference-based assembly using Illumina paired-end data. The complete cp genome is 156,342 bp in length, containing a large single-copy region of 85,459 bp, a small single-copy region of 18,785 bp, which are separated by a pair of inverted repeat regions of 26,049 bp, a total of 140 genes were predicted from the cp genome, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes . Most genes occur as a single copy, while 19 gene species are duplicated. Phylogenetic analysis reveals that R. laevigata and Rosa roxburghii f. normalis are more closely related to each other than either is to Rosa banksiae var. normalis.