The complete chloroplast genome sequence of Eriobotrya fragrans

Eriobotrya fragrans Champion ex Bentham is a potential medicinal plant of the genus Eriobotrya Lindl in the family Rosaceae. To better determine its phylogenetic location with respect to the other Rosaceae species, the complete chloroplast genome of E. fragrans was sequenced. The whole E. fragrans chloroplast genome is 159,286 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,343 bp, one large single-copy (LSC) region of 87,301 bp, and one small single-copy (SSC) region of 19,299 bp. The overall GC content of the whole chloroplast genome is 36.7%. Further, phylogenetic analysis using maximum likelihood with TVM + F+R2 model strongly supports the relationship: sisterhood of E. fragrans and E. japonica, followed by three species of Pyrus L

Complete plastome of a subtropical tree Eriobotrya malipoensis (Rosaceae) in Yunnan

Eriobotrya malipoensis Kuan is an important wild woody evergreen tree within the genus Eriobotrya Lindl belonging the family Rosaceae. To better determine its phylogenetic location with respect to the other Eriobotrya species, the complete plastome of E. malipoensis was sequenced. The whole plastome is 159,313 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,344 bp, one large single-copy (LSC) region of 87,270 bp, and one small single-copy (SSC) region of 19,355 bp. The overall G + C content of the whole plastome is 36.7%. Further, maximum likelihood phylogenetic analyse (TVM + F+R2 model) was conducted using 14 complete plastome of the Rosaceae. Our phylogeny supports the relationships: sisterhood of the E. malipoensis and E. fragrans Champ, flowed E. japonica Lindl

Complete Chloroplast Genome Sequence of <i>Rosa lucieae</i> and Its Characteristics

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa

Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa

The complete plastome sequence of a subtropical tree Pyrus betulaefolia (Rosaceae)

The genus Pyrus, comprising several popular fruit crops worldwide, includes over 30 tree species. Here we determined the complete plastid genome sequence of Pyrus betulaefolia. The plastome consists of 160,184 bp, including a pair of inverted repeats (IRs) with a length of 26,384 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) of 88,121 bp and 19,295 bp, respectively. Further phylogenetic analyze was conducted using 11 complete plastid genomes of Rosaceae with KVM + F + I model, which supports Pyrus betulaefolia as a sister to all other eight Pyrus taxa with published plastomes

Characteristics of the Complete Chloroplast Genome of Pourthiaea (Rosaceae) and Its Comparative Analysis

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159&ndash;160,401 bp, in which the large single copy was 88,047&ndash;88,359 bp, the small single copy was 19,234&ndash;19,338 bp, and the lengths of a pair of inverted repeats were 26,341&ndash;26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi &gt; 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea

Characteristics of the Complete Chloroplast Genome of <i>Pourthiaea</i> (Rosaceae) and Its Comparative Analysis

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159–160,401 bp, in which the large single copy was 88,047–88,359 bp, the small single copy was 19,234–19,338 bp, and the lengths of a pair of inverted repeats were 26,341–26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi > 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea

BcGR1.1, a Cytoplasmic Localized Glutathione Reductase, Enhanced Tolerance to Copper Stress in Arabidopsis thaliana

Copper is a mineral element, which is necessary for the normal growth and development of plants, but high levels of copper will seriously damage plants. Studies have shown that AtGR1 improves the tolerance of Arabidopsis to aluminum and cadmium stress. However, the role of GR in the copper stress response of plants is still unclear. Here, we identified four genes (named BcGR1.1, BcGR1.2, BcGR2.1 and BcGR2.2, respectively) encoding glutathione reductase (GR) in non-heading Chinese cabbage (Brassica campestris (syn. Brassica rapa) ssp. chinensis), which could be divided into two types based on the subcellular localization. Among them, BcGR1.1, which belonged to the cytoplasmic localization type, was significantly upregulated under copper stress. Compared to WT (the wild type), Arabidopsis thaliana heterologously overexpressed BcGR1.1 had longer roots, higher fresh weight, higher GSH levels and GSH/GSSG (oxidized form of GSH) ratio, and accumulated more superoxide dismutase and peroxidase under copper stress. However, in the AsA-GSH cycle under copper stress, the contents of AsA and AsA/DHA were significantly downregulated, and the contents of DHA and T-AsA (total AsA) were upregulated, in the BcGR1.1-overexpressing Arabidopsis. Therefore, BcGR1.1 could improve the scavenging ability of reactive oxygen species (ROS) by increasing the activity of GR, antioxidant enzymes and the utilization of AsA, and then enhance the copper stress tolerance of plants