Chloroplast Genome Structure Research Articles

The chloroplast genome comparative characteristic of artificial breeding tree, a case about Broussonetia kazinoki �Broussonetia papyrifera

Broussonetia kazinoki × Broussonetia papyrifera (ZJGS) is a hybrid species in Moraceae family, which has a very complicated hybrid origin. The excellent characteristics of fast growth, strong soil and water conservation ability, high leaf protein content and stem fiber content in ZJGS make it both ecological benefits in the mining area and economically valuable. This study aims to further understand ZJGS and other Moraceae taxa through the ZJGS chloroplast (cp) genome structure and the comparison with 12 closely related Moraceae species. Among the 13 Moraceae species, the cp genome length of seven Broussonetia species (ranges from 160,239 bp to 162,594 bp) is larger than that of six Morus species (ranges from 158,459 bp to 159,265 bp). Among the 77 shared protein-coding genes (PCGs) in Moraceae species, the obvious positive selection of Ka/Ks ratios acted on petD and rpl16 genes of B. kazinoki and B. papyrifera, respectively. Phylogenetic analysis based on shared PCGs from 28 species shows that ZJGS is closely related to maternal B. kazinoki. These findings provide data support for the origin of ZJGS hybridization and provide genomic resources for future ZJGS resource development and molecular breeding.

Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.).

The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922bp consisting of four conserved regions: a 5145bp small single-copy(SSC) region, a 91,323bp large single-copy(LSC) region, and two identical length-inverted repeat(IR) regions (39,725bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.

The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences

BackgroundAs one of the largest genera in Apiaceae, Bupleurum L. is well known for its high medicinal value. The genus has frequently attracted the attention of evolutionary biologist and taxonomist for its distinctive characteristics in the Apiaceae family. Although some chloroplast genomes data have been now available, the changes in the structure of chloroplast genomes and selective pressure in the genus have not been fully understood. In addition, few of the species are endemic to Southwest China, a distribution and diversity center of Chinese Bupleurum. Endemic species are key components of biodiversity and ecosystems, and investigation of the chloroplast genomes features of endemic species in Bupleurum will be helpful to develop a better understanding of evolutionary process and phylogeny of the genus. In this study, we analyzed the sequences of whole chloroplast genomes of 4 Southwest China endemic Bupleurum species in comparison with the published data of 17 Bupleurum species to determine the evolutionary characteristics of the genus and the phylogenetic relationships of Asian Bupleurum.ResultsThe complete chloroplast genome sequences of the 4 endemic Bupleurum species are 155,025 bp to 155,323 bp in length including a SSC and a LSC region separated by a pair of IRs. Comparative analysis revealed an identical chloroplast gene content across the 21 Bupleurum species, including a total of 114 unique genes (30 tRNA genes, 4 rRNA genes and 80 protein-coding genes). Chloroplast genomes of the 21 Bupleurum species showed no rearrangements and a high sequence identity (96.4–99.2%). They also shared a similar tendency of SDRs and SSRs, but differed in number (59–83). In spite of their high conservation, they contained some mutational hotspots, which can be potentially exploited as high-resolution DNA barcodes for species discrimination. Selective pressure analysis showed that four genes were under positive selection. Phylogenetic analysis revealed that the 21 Bupleurum formed two major clades, which are likely to correspond to their geographical distribution.ConclusionsThe chloroplast genome data of the four endemic Bupleurum species provide important insights into the characteristics and evolution of chloroplast genomes of this genu, and the phylogeny of Bupleurum.

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae.

The simple sequence repeats (SSRs) of plant chloroplasts show considerable genetic variation and have been widely used in species identification and phylogenetic relationship determination. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced, and their SSR characteristics were compared and statistically analyzed. The results showed that the chloroplast genome structure was highly conserved (genome size: 154,046–166,151 bp), and the gene content (117 genes) and gene order were highly consistent. The distribution characteristics of SSRs (number, relative abundance, relative density, GC content) showed taxon specificity. The primary results were the total numbers of SSRs and mononucleotides: Gymnosphaera (61–67 and 40–47, respectively), Alsophila (121–122 and 95–96), and Sphaeropteris (102–103 and 77–80). Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera. This study indicates that the distribution characteristics of Cyatheaceae chloroplast SSRs can provide useful phylogenic information at the genus level.

The complete chloroplast genome of Rhamnus crenata Siebold & Zuccarini (Rhamnaceae)

Rhamnus crenata Siebold & Zuccarini is deciduous shrub or small tree plant that widely distributed in temperate and tropical regions of East to Southeast Asia. It has a chloroplast genome structure similar to that of other species of Rhamnus. It is 160,454 bp in size, including a large single-copy (LSC) region of 88,884 bp, a small single-copy (SSC) region of 18,734 bp and a pair of inverted repeats (IRs) of 26,418 bp. A total of 122 genes were annotated, including 80 protein-coding genes, 38 transfer RNA (tRNA) genes, and 4 rRNA genes. The overall GC content is 30.71%. Phylogenetic analysis shows that R. crenata is clustered with R. taquetii and R. globosa.

Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications

BackgroundImpatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and horticultural value. However, knowledge about its germplasm identification, molecular phylogeny, and chloroplast genomics is limited, and taxonomic uncertainties still exist due to overlapping morphological features and insufficient genomic resources.ResultsWe sequenced the chloroplast genomes of six different species (Impatiens chlorosepala, Impatiens fanjingshanica, Impatiens guizhouensis, Impatiens linearisepala, Impatiens loulanensis, and Impatiens stenosepala) in the karst area of China and compared them with those of six previously published Balsaminaceae species. We contrasted genomic features and repeat sequences, assessed sequence divergence and constructed phylogenetic relationships. Except for those of I. alpicola, I. pritzelii and I. glandulifera, the complete chloroplast genomes ranging in size from 151,366 bp (I. alpicola) to 154,189 bp (Hydrocera triflora) encoded 115 distinct genes [81 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) genes]. Moreover, the characteristics of the long repeat sequences and simple sequence repeats (SSRs) were determined. psbK-psbI, trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified as divergence hotspot regions and thus might be suitable for species identification and phylogenetic studies. Additionally, the phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) of the whole chloroplast genomes showed that the chloroplast genome structure of I. guizhouensis represents the ancestral state of the Balsaminaceae family.ConclusionOur study provided detailed information about nucleotide diversity hotspots and the types of repeats, which can be used to develop molecular markers applicable to Balsaminaceae species. We also reconstructed and analyzed the relationships of some Impatiens species and assessed their taxonomic statuses based on the complete chloroplast genomes. Together, the findings of the current study might provide valuable genomic resources for systematic evolution of the Balsaminaceae species.

The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae.

Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relationships of Crassulaceae remain partially obscured. Here, we report nine newly sequenced chloroplast genomes, which comprise several key lineages of Crassulaceae. Our comparative analyses and positive selection analyses of Crassulaceae species indicate that the overall gene organization and function of the chloroplast genome are highly conserved across the family. No positively selected gene was statistically supported in Crassulaceae lineage using likelihood ratio test (LRT) based on branch-site models. Among the three subfamilies of Crassulaceae, our phylogenetic analyses of chloroplast protein-coding genes support Crassuloideae as sister to Kalanchoideae plus Sempervivoideae. Furthermore, within Sempervivoideae, our analyses unambiguously resolved five clades that are successively sister lineages, i.e., Telephium clade, Sempervivum clade, Aeonium clade, Leucosedum clade, and Acre clade. Overall, this study enhances our understanding of the infrafamilial relationships and the conservation of chloroplast genomes within Crassulaceae.

The complete chloroplast genome of Atractylodes japonica Koidz. ex Kitam. and its phylogenetic inference

Atractylodes japonica Koidz. ex Kitam. is a perennial herbal plant, and its dried rhizomes have been widely used as traditional medicine in China and Japan. In this study, we assembled and annotated the complete chloroplast (cp) genome sequence of A. japonica using the high-throughput sequencing approach. The cp genome of A. japonica is 153,208 bp in length with the overall GC content of 37.7%, including two inverted repeat (IR) regions of 25,147 bp, which was separated by a large single-copy (LSC) region of 84,255 bp and a small single-copy (SSC) region of 18,659 bp. 113 unique genes were annotated in the genome, including 80 protein-coding genes, 29 represented tRNA genes, and four denoted rRNA genes. A maximum-likelihood phylogenetic analysis with 38 complete cp sequences showed that Atractylodes formed a monophyletic clade, and A. japonica and A. koreana formed a subclade in Atractylodes. This study provides the chloroplast genome structure features and phylogenetic relationship of A. japonica.

Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

BackgroundMyrtales 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.ResultsA 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).ConclusionsThe 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.

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

Structure and variation analyses of chloroplast genomes in Carpinus

Structure and variation analyses of chloroplast genomes in Carpinus

The complete chloroplast genome of Phyllostachys edulis f. curviculmis (Bambusoideae): a newly ornamental bamboo endemic to China

Phyllostachys edulis (Bambusoideae) is a temperate woody bamboo with a long history of cultivation in China. Phyllostachys edulis f. curviculmis is the latest new forma that repored in 2018. Here, we performed the complete chloroplast genomes of P. edulis and P. edulis f. curviculmis using genome skimming. The length of two chloroplast genomes was 139,678 bp, and their GC contents were 38.9%. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Moreover, in subspecies-level, P. edulis ‘Pachyloen’ and P. edulis f. curviculmis are identical to P. edulis in the terms of chloroplast genome size, structure, and composition, further indicating their affinity.

Complete chloroplast genome of Saussurea inversa (Asteraceae) and phylogenetic analysis

Saussurea inversa Raab-Straube is a small perennial and polycarpic herb that is distributed on the rocky slopes of the Qinghai-Tibetan plateau (QTP) at an altitude of 3700–5400 meters. It has a chloroplast genome structure similar to that of other species of Saussurea. It is 152,102 bp in size, including a large single-copy (LSC) region of 83,450 bp, a small single-copy (SSC) region of 18,286 bp and a pair of inverted repeats (IRs) of 25,183 bp. The chloroplast genome of S. inversa encodes 113 genes, containing 80 protein-coding genes (PCGs), 29 tRNA and four rRNA genes. Phylogenetic analysis shows that S. inversa is clustered with S. pseudosimpsoniana and S. laniceps.

The Complete Chloroplast Genome Sequence of <i>Viburnum odoratissimum</i> and Phylogenetic Relationship with Other Close Species in the Adoxaceae Family

The chloroplast genome structure and gene content are highly conserved among land plants, providing valuable information for the studies of taxonomy and plant evolution. Viburnum odoratissimum is a well-known evergreen shrub widely distributed in Asia. It possesses excellent medicinal properties used as traditional medicine for menstrual, stomach, and kidney cramps. In this study, the complete chloroplast genome (cpDNA) of V. odoratissimum is reported and compared with five close Viburnum species and an outgroup. The cpDNA of V. odoratissimum is 158,744 bp in length and contains 130 genes with 17 genes duplicated in the inverted repeat region. The gene content, gene organization and GC content in V. odoratissimum are highly similar to other Viburnum species. A total of 270 tandem repeats is found in these plastomes, most of which are distributed in intergenic space. Differences in the location of the IR/SC boundaries reflect expansions and contractions of IR regions in all species studied. Phylogenetic analysis based on complete chloroplast genomes and the combination of barcodes indicates a sister relationship between V. odoratissimum and V. brachybotryum. Furthermore, a comparative cpDNA analysis identifies three DNA regions (trnC-petN-psbM, trnH-psbA, ndhC-trnV) containing high divergence among seven studied species that could be used as potential phylogenetic markers in taxonomic studies.

Sequencing of Complete Chloroplast Genomes.

In this chapter, frequently used methods for elucidating sequence and structure of chloroplast genomes are reviewed, as a current best practice guide. This concerns methods for DNA extraction, sequencing library preparation, and bioinformatics (assembly, verification, annotation, and sequence comparisons). Recommendations for standard data reporting practices are given-chloroplast genome sequencing reports can be highly formalized, and publication in the form of standard data reports is the best option for comparison and meta-analysis purposes.

Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

BackgroundOat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species.ResultsThe chloroplast genomes of eleven Avena species (size range of 135,889–135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014–80,132 bp), a small single copy (SSC; 12,575–12,679 bp) and a pair of inverted repeats (IRs; 21,603–21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus.ConclusionsDiversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.

Characterization of the complete chloroplast genome sequence of the endangered species Platycrater arguta (Hydrangeaceae)

Platycrater arguta is a rare and endangered shrub species endemic to East Asia. Here, we report the complete chloroplast (cp) genome structure and its taxonomic position within Hydrangeaceae to promote its conservation and restoration. The complete cp genome of P. arguta was 157,810 bp in length and contained a large single-copy region (LSC) of 86,823 bp and a small single-copy region (SSC) of 18,735 bp, as well as a pair of inverted repeat (IR) regions of 26,126 bp, each. 113 unique genes are predicted in this cp genome, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and 4 rRNAs. Maximum-likelihood (ML) phylogenetic analysis based on 79 shared cp CDS (coding DNA sequences) of 19 species reveals a close relationship between P. arguta and Schizophragma hydrangeoides.

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae.

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

Structural characterization and comparative analysis of the chloroplast genome of Ginkgo biloba and other gymnosperms

Ginkgo biloba is a famous living “fossil” and has played an important role in the evolution of the Plant Kingdom. Here, the complete chloroplast genome of G. biloba was sequenced and analysed. The chloroplast genome was 156,990 bp long and predicted to encode 134 genes including 85 protein-coding genes, 41 tRNA genes and 8 rRNA genes. The chloroplast genome has a typical quadripartite structure with a pair of inverted repeat regions (IRa and IRb, 17,732 bp), a large (LSC, 99,259 bp) and small single (SSC, 22,267 bp) copy region. After an extensive comparison to previously published gymnosperm plastomes, the gene content and organisation of G. biloba showed high divergence, although part was relatively conserved. The two typical IR regions in the G. biloba chloroplast genome were relatively shorter because it the ycf2 gene. In addition, it was obvious that the IR regions and gene loss were responsible for changes in chloroplast genome size and structure stability, which influenced plastome evolution in different gymnosperms. Phylogenetic analysis revealed that G. biloba is sister to cycads rather than to gnetophytes, cupressophytes, and Pinaceae. Overall, the study showed that the genomic characteristics of G. biloba would be of great help in the further research on the taxonomy, species identification and evolutionary history of gymnosperms, especially for their position in plant systematics and evolution.

Two plastomes of Phyllostachys and reconstruction of phylogenic relationship amongst selected Phyllostachys species using genome skimming

The genus Phyllostachys is economically important; however, only a small amount of complete plastid genomes have been reported to date. Here, we characterized two complete chloroplast genomes of Phyllostachys using genome skimming. The chloroplast genomes of Phyllostachys reticulata and Phyllostachys edulis ‘Pachyloen’ were 136,689 bp and 139,678 bp in length, respectively, and their GC contents were 38.8% and 38.9%, respectively. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Phylogenetic analysis shows that all selected Phyllostachys species were grouped into one well-supported clade in the Phyllostachys clade (V) of Arundinarieae. Moreover, in terms of chloroplast genome size, structure, and composition, P. edulis ‘Pachyloen’ is identical to P. edulis, further indicating the affinity between them.