Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

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Comparative Chloroplast Genome Analyses of Ilex (Aquifoliaceae): Insights Into Evolutionary Dynamics and Phylogenetic Relationships

10.21203/rs.3.rs-930025/v1 ◽

2021 ◽

Author(s):

Kewang Xu ◽

Chenxue Lin ◽

Shiou Yih Lee ◽

Lingfeng Mao ◽

Kaikai Meng

Keyword(s):

Chloroplast Genome ◽

Genome Evolution ◽

Dna Barcoding ◽

Phylogenetic Relationships ◽

Evolutionary Dynamics ◽

Genome Structure ◽

Gc Content ◽

Chloroplast Genome Evolution ◽

Chloroplast Genomes ◽

Mutational Hotspots

Abstract BackgroundDespite many species of Ilex (Aquifoliaceae) are of horticultural importance and are widely grown in parks and gardens throughout the world for their foliage and decorative berries, limited genetic information has greatly hampered our understanding of the chloroplast genome evolution and phylogenetic relationships within the genus. This study attempted to address these problems by comparing the chloroplast genomes and analyzing phylogenetic relationships within the genus.ResultsIn this study, analyses of chloroplast genome structure, codon usage, GC content, gene rearrangement, nucleotide diversity, inverted repeats (IR) boundary, repeat sequence, and SSR component were conducted by comparing 41 chloroplast genomes of Ilex. The results showed that these Ilex chloroplast genomes were evolutionary conserved at the genome level and no rearrangement of the complete cp genome in the 41 Ilex genomes was recorded. On the contrary, there were still a few mutational hotspots identified from these chloroplast genomes, which were considered as hypervariable regions useful for future phylogenetic studies and DNA barcoding. Using the complete chloroplast genome sequences, we reconstructed a highly supported phylogeny of Ilex and well-resolved the complicated relationships among the different lineages within Ilex.ConclusionThe present study increased our understanding of the chloroplast genome evolution and phylogenetic relationships within Ilex. The availability of these genetic resources will be helpful for the future studies in DNA barcoding, species delimitation, phylogenetic reconstruction as well as the hybridization and introgression events between distantly related lineages within Ilex.

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Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Forests ◽

10.3390/f11030309 ◽

2020 ◽

Vol 11 (3) ◽

pp. 309

Author(s):

Konrad Celiński ◽

Hanna Kijak ◽

Justyna Wiland-Szymańska

Keyword(s):

Chloroplast Genome ◽

Canary Islands ◽

Genome Structure ◽

Gc Content ◽

Phylogenetic Inference ◽

Single Copy ◽

Genetic Identification ◽

Chloroplast Genomes ◽

Mutational Hotspots ◽

Dracaena Draco

Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

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Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

BMC Plant Biology ◽

10.1186/s12870-021-02985-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xiao-Feng Zhang ◽

Jacob B. Landis ◽

Hong-Xin Wang ◽

Zhi-Xin Zhu ◽

Hua-Feng Wang

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Divergence Time ◽

Gc Content ◽

Single Copy ◽

Molecular Dating ◽

Rrna Genes ◽

Chloroplast Structure ◽

Chloroplast Genomes ◽

Part Structure

Abstract Background Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. Results A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214–171,315 bp and exhibit a typical four part structure. The IR region is between 23,901–36,747 bp, with the large single copy region spanning 83,691–91,249 bp and the small single copy region spanning 11,150–19,703 bp. In total, 123–133 genes are present in the chloroplasts including 77–81 protein coding genes, four rRNA genes and 30–31 tRNA genes. The GC content was 36.9–38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7–37.3%, 30.6–36.8% and 39.7–43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88–114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50–118.62 Ma). Conclusions The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

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Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Frontiers in Genetics ◽

10.3389/fgene.2021.709996 ◽

2021 ◽

Vol 12 ◽

Author(s):

Abbas Jamal ◽

Jun Wen ◽

Zhi-Yao Ma ◽

Ibrar Ahmed ◽

Abdullah ◽

...

Keyword(s):

Chloroplast Genome ◽

Eastern China ◽

Gc Content ◽

Quaternary Period ◽

Medicinal Uses ◽

Endemic Genus ◽

Chloroplast Genomes ◽

Genome Features ◽

Forest Regions ◽

Genome Analyses

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

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The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽

10.3390/molecules24020261 ◽

2019 ◽

Vol 24 (2) ◽

pp. 261 ◽

Cited By ~ 8

Author(s):

Yongfu Li ◽

Steven Paul Sylvester ◽

Meng Li ◽

Cheng Zhang ◽

Xuan Li ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Genome Structure ◽

Phylogenetic Reconstruction ◽

Strong Support ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Critically Endangered Species ◽

Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽

10.3390/plants9010061 ◽

2020 ◽

Vol 9 (1) ◽

pp. 61 ◽

Cited By ~ 5

Author(s):

Huyen-Trang Vu ◽

Ngan Tran ◽

Thanh-Diem Nguyen ◽

Quoc-Luan Vu ◽

My-Huyen Bui ◽

...

Keyword(s):

Chloroplast Genome ◽

Inverted Repeat ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Complete Chloroplast Genome ◽

Critically Endangered Species ◽

Plastid Genomes ◽

Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

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Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants

Genome Biology and Evolution ◽

10.1093/gbe/evz256 ◽

2019 ◽

Cited By ~ 1

Author(s):

Weiwen Wang ◽

Robert Lanfear

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Single Copy ◽

Land Plant ◽

Inverted Repeats ◽

Individual Plant ◽

Single Individual ◽

Equal Frequency ◽

Flip Flop ◽

Chloroplast Genomes

Abstract The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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Comparative Chloroplast Genome Analysis of Medicinally Important Veratrum (Melanthiaceae) in China: Insights into Genomic Characterization and Phylogenetic Relationships

10.21203/rs.3.rs-117897/v1 ◽

2020 ◽

Author(s):

Ying-min Zhang ◽

Li-jun Han ◽

Ying-Ying Liu ◽

Cong-wei Yang ◽

Xing Tian ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Blood Stasis ◽

Genome Comparison ◽

Phylogenetic Study ◽

Species Classification ◽

Chloroplast Genomes ◽

Genomic Characterization ◽

Cp Genome

Abstract Background: Veratrum is a genus of perennial herbs that are widely used as traditional Chinese medicine for emetic, resolving blood stasis and relieve pain. However, the species classification and the phylogenetic relationship of the genus Veratrum have long been controversial due to the complexity of morphological variations. Knowledge on the infrageneric relationships of the genus Veratrum can be obtained from their chloroplast genome sequences and increase the taxonomic and phylogenetic resolution.Methods: Total DNA was extracted from ten species of Veratrum and subjected to next-generation sequencing. The cp genome was assembled by NOVOPlasty. Genome annotation was conducted using the online tool DOGMA and subsequently corrected by Geneious Prime. Then, genomic characterization of the Veratrum plastome and genome comparison with closely related species was analyzed by corresponding software. Moreover, phylogenetical trees were reconstructed, based on the 29 plastomes by maximum likelihood (ML) and Bayesian inference (BI) methods.Results: The whole plastomes of Veratrum species possess a typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising 135 genes. The gene order, content, and genome structure were nearly identical with a few exceptions across the Veratrum chloroplast genomes. The total number of simple sequence repeats (SSRs) ranged from 31 to 35, and of large sequence repeats (LSRs) ranged from 65 to 71. Seven highly divergent regions (rpoB-trnC, trnT-trnL, trnS-trnG, psbC-psbZ, psbI, ycf1, and ndhF) were identified that can be used for DNA barcoding in the genus of Veratrum. Phylogenetic analyses based on 29 plastomes strongly supported the monophyly of Veratrum. The circumscription and relationships of infrageneric taxa of Veratrum were well evaluated with high resolutions. Conclusions: Our study identified and analyzed the cp genome features of ten Veratrum species, and suggested high effectivity of chloroplast complete genome in resolving generic circumscription in Veratrum. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the phylogenetic study of Melanthiaceae simultaneously.

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Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis—“Wild Plants with a Tiny Population”—and Three Other Pyrus Species

International Journal of Molecular Sciences ◽

10.3390/ijms19103262 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3262 ◽

Cited By ~ 9

Author(s):

Yongtan Li ◽

Jun Zhang ◽

Longfei Li ◽

Lijuan Gao ◽

Jintao Xu ◽

...

Keyword(s):

Chloroplast Genome ◽

Population Decline ◽

Gc Content ◽

Single Copy ◽

Wild Plants ◽

Similar Degree ◽

Protein Coding ◽

Chloroplast Genomes ◽

Close Relationship ◽

History Of

Pyrus hopeiensis is a valuable wild resource of Pyrus in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the “wild plants with a tiny population” in China. To date, few studies have been conducted on P. hopeiensis. This paper offers a systematic review of P. hopeiensis, providing a basis for the conservation and restoration of P. hopeiensis resources. In this study, the chloroplast genomes of two different genotypes of P. hopeiensis, P. ussuriensis Maxin. cv. Jingbaili, P. communis L. cv. Early Red Comice, and P. betulifolia were sequenced, compared and analyzed. The two P. hopeiensis genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of P. hopeiensis HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of P. hopeiensis HB-2. The lengths of the SSC and IR regions of the two Pyrus genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in P. hopeiensis HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of P. hopeiensis were similar to those of the other three Pyrus species. The IR boundary of the two genotypes of P. hopeiensis showed a similar degree of expansion. To determine the evolutionary history of P. hopeiensis within the genus Pyrus and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera Pyrus and Malus, and the relationship between P. hopeiensis HB-1 and P. hopeiensis HB-2 was the closest.

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