Chloroplasts are at the front line of many advancements in molecular biology, ranging from evolutionary biology to the mechanism of energy transduction, also including stress responses and programmed ...leaf death. In addition to the relevance of basic knowledge, advances are unveiling promising insights to improve plant productivity, disease resistance, and environmental control. The production of secondary metabolites and proteins by transformed chloroplasts adds further excitement to applied investigations on chloroplasts.
The comparison of the sequences of the chloroplast DNA of different plants provides valuable information on gene content, reordering in the circular chloroplast DNA, and mutational genetic-derive, relevant to the evolution of the chloroplast. Increasing facilities for intense genome sequencing have prompted many laboratories to focus on the chloroplast DNA. Reflecting these efforts, more than half of the articles in this book deal with functional or evolutionary investigations based on sequence analyses of chloroplast DNA. Additional topics treated in the issue include post-transcriptional control, the processing of nuclear encoded preproteins of chloroplasts, the response of photosynthetic machinery to water deficit, turn-over of chloroplast proteins, mechanism of chloroplast division, and chloroplast movements.
Zingiberaceae is taxonomically complex family where species are perennial herb. However, lack of chloroplast genomic information severely hinders our understanding of Zingiberaceae species in the ...research of evolution and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of fourteen
species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the 25 Zingiberaceae species. In each Zingiberaceae species, the 25 complete chloroplast genomes ranging from 155,890 bp (
) to 164,101 bp (
) contained 111 genes consisting of 77 protein coding genes, 4 ribosomal RNAs and 30 transfer RNAs. These chloroplast genomes are similar to most angiosperm that consisted of a four-part circular DNA molecules. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Six divergent hotspots regions (
,
,
,
,
, and
) were identified in the 25 Zingiberaceae chloroplast genomes, which could be potential molecular markers. In addition to
, the ψ
was discovered among the 25 Zingiberaceae species. The shared protein coding genes from 52 Zingiberales plants and four other family species as out groups were used to construct phylogenetic trees distinguished by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) and showed that Musaceae was the basal group in Zingiberales, and
had a close relationship with
. Besides this,
was clustered together with
. Its distribution area (Southeast Asia) overlaps with the latter. Maybe hybridization occur in related groups within the same region. This may explain why Zingiberaceae species have a complex phylogeny, and more samples and genetic data were necessary to confirm their relationship. This study provide the reliable information and high-quality chloroplast genomes and genome resources for future Zingiberaceae research.
Analysis of the relationships among wild species of section
Moutan
in the plant genus
Paeonia
has traditionally been problematic. Interspecies relationships cannot be effectively determined using ...phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast genome sequences will aid the identification and phylogeny of these species. In this study, the complete chloroplast genomes of three sect.
Moutan
plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect.
Moutan
were then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single copy (LSC) regions were considerably greater than those in the inverted repeat (IR) regions. Phylogenetic analysis revealed that the species of sect.
Moutan
clustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study,
Paeonia jishanensis
clustered with another
P. jishanensis
sequence from the GenBank database,
Paeonia qiui
clustered with
Paeonia rockii
, and
Paeonia delavayi
var.
lutea
clustered with
Paeonia ludlowii
. It was also found that the complete chloroplast genomes, LSC regions, and SSC regions all showed great abilities in identification and phylogenetic analysis of the species of sect.
Moutan
, while IRs regions and highly variable regions were not suitable for the species of sect.
Moutan
.
Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related ...species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships.
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide ...a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at
https://irscope.shinyapps.io/chloroplot/
.
Dendrobium williamsonii and Dendrobium cariniferum (Orchidaceae) are endangered perennial herbs, and they are very similar in morphology. Chloroplast genome sequencing technology provides a powerful ...tool for molecular analysis to get more infomation for phylogenetic analysis and identification of Dendrobium species. In this study, the complete chloroplast genomes of Dendrobium williamsonii and Dendrobium cariniferum were assembled and characterized using Illumina NovaSeq 6000. The genome sizes are 159 695 and 159 479 bp, including pairs of inverted repeats (27 055 and 27 024 bp) each separated by small single-copy regions (18 451 and 18 488 bp) and large single-copy regions (87 134 and 86 943 bp). The chloroplast genome overall GC content was 37.11% and 37.13%, respectively. Each chloroplast genome encoded the same number (147) of genes, including 88 protein-coding genes, 51 tRNA genes, and 8 rRNA genes. Comparative analysis of chloroplast genomes revealed the high degree of divergence included accD-psaL and ycf4 -cemA. The phylogenetic tree showed the two Dendrobium species formed only one small clade. A pair of primers that could effectively identify the two Dendrobium species were also screened. This study will provide theoretical basis for species identification, genetic breeding, and evolution of Dendrobium.
Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina ...sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants.
The black locust (Robinia pseudoacacia) is widely distributed, and has strong drought resistance and salt tolerance. These characteristics make it the best type of tree for landscaping and resource ...conservation in China. In this study, the chloroplast genomes of five black locusts were identified de novo and the evolutionary relationship among these black locusts and their taxonomic statuses in leguminous plants were determined. The chloroplast structures of the five black locusts were typical and had four parts, including two single copy regions (large and small single copy sections) and a pair of inverted repeats (IRs). Genome sizes were between 155,364 bp and 155,655 bp; the genome of R. pseudoacacia var. decaisneana was the smallest, while that of R. pseudoacacia var. tortuosa was the largest. The genomes contained 124–130 protein-coding genes; R. pseudoacacia var. tortuosa had the fewest, while R. hispida and R. pseudoacacia var. decaisneana had the most. In this study, eight to ten genes from chloroplast genomes contained introns. Nine genes from the chloroplast genomes of R. pseudoacacia and R. pseudoacacia f. unifolia contained introns that had lost the trnL-CAA gene via evolution, while eight chloroplast genes of R. pseudoacacia var. tortuosa contained introns that had lost the trnL-CAA and psaA genes. Among them, the rpoC1 gene had the longest introns at 2828 bp, and rps12+ had the smallest introns at only 533 bp. There were various amplification phenomena in the IR region among the five black locusts. Most of the protein-coding genes of the five black locusts had a high degree of codon preference. To determine the phylogenetic positions of the five black locusts, we conducted a systematic evolutionary analysis using common protein-coding genes in chloroplast sequences from 34 species of leguminous plants and 12 other species. The results showed that the relationship between Robinia and Acacia ligulata was the most distant among those of the leguminous plants, and the relationship between Robinia and Lotus japonicus was the closest. The chloroplast protein-coding genes in different black locusts were relatively conservative by evolutionary selection pressure analysis standards. These results are important for our understanding of their photosynthetic mechanisms and evolution, and the transgenic engineering of their chloroplasts.
•The research on molecular biology of the black locust is weak, and its phylogenetic position among plants remains unclear.•In this study, the chloroplast genomes of five black locusts were identified de novo.•The taxonomic statuses of black locusts in leguminous plants were determined.•The results are important for our understanding of their photosynthetic mechanisms and evolution.
Herein, we determined and analyzed the chloroplast (cp) genome sequence of Lonicera harae for the first time. The chloroplast genome was 154,959 bp and contained a large single copy (LSC) of ...approximately 88,849 bp as well as a small single copy (SSC) of 18,832 bp separated by a pair of 23,639 bp inverted repeats (IRs). The overall G+C content in the L. harae chloroplast genome was 38.4%. A total of 114 unique genes were annotated, comprising 80 protein-coding genes (PCGs), 30 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). Of these, 17 contained one or two introns. Phylogenetic analysis of 54 accessions revealed that L. harae forms a clade with L. fragrantissima. This newly sequenced chloroplast genome provides valuable molecular phylogenomic information for future studies to determine the taxonomic position of L. harae and the phylogenetic relationships within the genus Lonicera.
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•Chloroplast (cp) genomes of 35 species representing 31 genera of the 14 tribes of the Ranunculaceae were sequenced, based on which well-resolved phylogenetic trees were obtained.•Two ...waves of radiation within the core Ranunculaceae were identified, through which most of the extant tribes and genera were generated.•Many of the characters that were once widely used for systematic considerations were actually results of parallel, convergent or reversal evolution.•Frequent inversions, duplications, or losses of fragments have contributed to cp genome evolution.
The family Ranunculaceae, a member of early-diverging eudicots that is increasingly being used as a model for the study of plant developmental evolution, has been the focus of systematic studies for centuries. Recent studies showed that the family can be divided into 14 tribes, with Glaucideae, Hydrastideae, and Coptideae being the successive basal-most lineages. The relationships among the remaining 11 tribes, however, remain controversial, so that a clear picture of character evolution within the family is still lacking. In this study, by sequencing, assembling and analyzing the chloroplast (cp) genomes of 35 species representing 31 genera of the 14 tribes, we resolved the relationships among the tribes and genera of the Ranunculaceae and clarified several long-standing controversies. We found that many of the characters that were once widely used for taxonomic and systematic considerations were actually results of parallel, convergent or even reversal evolution, suggestive of unreliability. We also found that the family has likely experienced two waves of radiative evolution, through which most of the extant tribes and genera were generated. Notably, both waves of radiation were correlated with the increase in the temperature of the earth, suggesting that global warming may have been the driving force of the radiation events. Based on these observations, we hypothesize that global warming and the associated decrease in the type and number of animal pollinators may have been the main reason why taxa with highly elaborate petals as well as those without petal were generated during each of the two waves of radiation.
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