Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae)

Assembly and comparative analysis of the first complete mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria): insights into its genetic architecture and evolutionary relationships

Introduction

Zicaitai (Brassica rapa var. purpuraria) is a Brassica variety renowned for its distinctive taste and rich nutritional profile. In recent years, the mitochondrial genomes of several Brassica species have been documented, but the mitogenome of Zicaitai remains unreported.

Methods

In this study, we characterized the Zicaitai mitogenome achieved through the assembly of sequencing reads derived from both the Oxford Nanopore and Illumina platforms. A detailed comparative analysis was carried out with other Brassica species to draw comparisons and contrasts. In-depth analyses of codon usage patterns, instances of RNA editing, and the prevalence of sequence repeats within the mitogenome were also conducted to gain a more nuanced understanding of its genetic architecture. A phylogenetic analysis was performed, utilizing the coding sequences (CDS) from the mitochondrial genome of Zicaitai and that of 20 closely related species/varieties to trace evolutionary connections.

Results

The Zicaitai mitogenome is characterized by a circular structure spanning 219,779 base pairs, and it encompasses a total of 59 genes. This gene set includes 33 protein-coding genes, 23 tRNA genes, and 3 rRNA genes, providing a rich foundation for further genomic study. An analysis of the Ka/Ks ratios for 30 protein-coding genes shared by the mitogenomes of Zicaitai and seven other Brassica species revealed that most of these genes had undergone purifying selection. Additionally, the study explored the migration of genes between the chloroplast and nuclear genomes and the mitogenome, offering insights into the dynamics of genetic exchange within the Brassica genus.

Discussion

The collective results in this study will serve as a foundational resource, aiding future evolutionary studies focused on B. rapa, and contributing to a broader understanding of the complexities of plant evolution.

Assembly and comparative analysis of the first complete mitochondrial genome of Salix psammophila, a good windbreak and sand fixation shrub

Salix psammophila, commonly known as the sandlive willow, is a vital shrub species within the Salicaceae family, particularly significant for its ecological role in regions susceptible to desertification and sandy soils. In this study, we assembled the complete S. psammophila mitochondrial genome using Pacbio HiFi third-generation sequencing data. The genome was found to be a typical single circular structure, with a total length of 715,555 bp and a GC content of 44.89%. We annotated 33 unique protein-coding genes (PCGs), which included 24 core mitochondrial genes and 9 variable genes, as well as 18 tRNA genes (5 of which were multicopy genes) and 3 rRNA genes. Comparative analysis of the PCGs from the mitochondrial genomes of S. psammophila, Populus deltoides, Populus simonii, Salix wilsonii, and Salix suchowensis revealed that these genes are relatively conserved within the Salicaceae family, with variability primarily occurring in the ribosomal protein genes. The absence of the rps14, which encodes a ribosomal protein, may have played a role in the evolution of stress tolerance in Salicaceae plants. Additionally, we identified 232 SSRs, 19 tandem repeat sequences, and 236 dispersed repeat sequences in the S. psammophila mitochondrial genome, with palindromic and forward repeats being the most abundant. The longest palindromic repeat measured 260 bp, while the longest forward repeat was 86,068 bp. Furthermore, 324 potential RNA editing sites were discovered, all involving C-to-U edits, with the nad4 having the highest number of edits. These findings provide valuable insights into the phylogenetic and genetic research of Salicaceae plants.

Comparative analysis of the mitochondrial genomes of four Dendrobium species (Orchidaceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

The genus Dendrobium, part of the Orchidaceae family, encompasses species of significant medicinal, nutritional, and economic value. However, many Dendrobium species are threatened by environmental stresses, low seed germination rates, and overharvesting. Mitochondria generate the energy necessary for various plant life activities. Despite their importance, research on the mitochondrial genomes of Dendrobium species is currently limited. To address this gap, we performed a comprehensive genetic analysis of four Dendrobium species-D. flexicaule, D. nobile, D. officinale, and D. huoshanense-focusing on their mitochondrial and chloroplast genomes to elucidate their genetic architecture and support conservation efforts. We utilized advanced sequencing technologies, including Illumina for high-throughput sequencing and Nanopore for long-read sequencing capabilities. Our findings revealed the multichromosomal mitochondrial genome structures, with total lengths ranging from 596,506 bp to 772,523 bp. The mitochondrial genomes contained 265 functional genes, including 64-69 protein-coding genes, 23-28 tRNA genes, and 3 rRNA genes. We identified 647 simple sequence repeats (SSRs) and 352 tandem repeats, along with 440 instances of plastid-to-mitochondrial gene transfer. Additionally, we predicted 2,023 RNA editing sites within the mitochondrial protein-coding genes, predominantly characterized by cytosine-to-thymine transitions. Comparative analysis of mitochondrial DNA across the species highlighted 25 conserved genes, with evidence of positive selection in five genes: ccmFC, matR, mttB, rps2, and rps10. Phylogenetic assessments suggested a close sister relationship between D. nobile and D. huoshanense, and a similar proximity between D. officinale and D. flexicaule. This comprehensive genomic study provides a critical foundation for further exploration into the genetic mechanisms and biodiversity of Dendrobium species, contributing valuable insights for their conservation and sustainable utilization.

Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica)

Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.

The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae)

Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni. This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.

Assembly and comparative analysis of the complete mitochondrial genome of Isopyrum anemonoides (Ranunculaceae)

Ranunculaceae is a large family of angiosperms comprising 2500 known species-a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I. anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum. The circular mitogenome of I. anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I. anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I. anemonoides, including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes (nad1 and rpl5) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites (atp6 and mttB) were detected in the I. anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I. anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I. anemonoides. Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I. anemonoides.

Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

BACKGROUND

The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.

RESULTS

It was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.

CONCLUSIONS

The results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.

Virus-Induced Gene Silencing (VIGS) in Chinese Jujube

Virus-induced gene silencing (VIGS) is a fast and efficient method for assaying gene function in plants. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully practiced in some species such as cotton and tomato. However, little research of VIGS systems has been reported in woody plants, nor in Chinese jujube. In this study, the TRV-VIGS system of jujube was firstly investigated. The jujube seedlings were grown in a greenhouse with a 16 h light/8 h dark cycle at 23 °C. After the cotyledon was fully unfolded, Agrobacterium mixture containing pTRV1 and pTRV2-ZjCLA with OD₆₀₀ = 1.5 was injected into cotyledon. After 15 days, the new leaves of jujube seedlings showed obvious photo-bleaching symptoms and significantly decreased expression of ZjCLA, indicating that the TRV-VIGS system had successfully functioned on jujube. Moreover, it found that two injections on jujube cotyledon could induce higher silencing efficiency than once injection. A similar silencing effect was then also verified in another gene, ZjPDS. These results indicate that the TRV-VIGS system in Chinese jujube has been successfully established and can be applied to evaluate gene function, providing a breakthrough in gene function verification methods.

Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae

BACKGROUND

Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed.

RESULTS

The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis.

CONCLUSIONS

In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea

Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinnabari and performed comparative genomics of nine genomes of the genus Dracaena. The results showed that the genome sizes range from 155,055 (D. elliptica) to 155,449 (D. cochinchinensis). The cp genomes of D. serrulata and D. cinnabari encode 131 genes, each including 85 and 84 protein-coding genes, respectively. However, the D. hokouensis had the highest number of genes (133), with 85 protein coding genes. Similarly, about 80 and 82 repeats were identified in the cp genomes of D. serrulata and D. cinnabari, respectively, while the highest repeats (103) were detected in the cp genome of D. terniflora. The number of simple sequence repeats (SSRs) was 176 and 159 in D. serrulata and D. cinnabari cp genomes, respectively. Furthermore, the comparative analysis of complete cp genomes revealed high sequence similarity. However, some sequence divergences were observed in accD, matK, rpl16, rpoC2, and ycf1 genes and some intergenic spacers. The phylogenomic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, sister to the remaining Dracaena species sampled in this study, with high bootstrap values. In conclusion, this study provides valuable genetic information for studying the evolutionary relationships and population genetics of Dracaena, which is threatened in its conservation status.

"Omics" insights into plastid behavior toward improved carotenoid accumulation

Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

BACKGROUND

Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species.

RESULTS

The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae.

CONCLUSION

All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.

Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae

BACKGROUND

The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae.

RESULTS

The chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species.

CONCLUSION

Orchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.

Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid

BACKGROUND

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored.

RESULTS

We characterized the A. truncatum mitogenome, which was assembled using reads from PacBio and Illumina sequencing platforms, performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052 bp, with a base composition of 27.11% A, 27.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. In addition, the gene migration from chloroplast and nuclear genomes to the mitogenome were analyzed. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species.

CONCLUSIONS

In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which would facilitate evolutionary research and molecular barcoding in Acer.

Plastome Diversity and Phylogenomic Relationships in Asteraceae

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae-as well as in the sister family Calyceraceae-lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family's phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Background

The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.

Results

The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.

Conclusions

Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08006-1.

The complete chloroplast genome sequence of Ziziphus attopensis (Rhamnaceae) and its phylogenetic analysis

Ziziphus attopensis has high medicinal value of tonic, carminative, appetizer, and muscle analgesic. To provide genetic information for further research and conservation, the complete chloroplast genome sequence of Z. attopensis was determined in this study. The genome was 161,342 bp in length, consisting of a large single copy region (89,035 bp), a small single copy region (19,421 bp), and a pair of inverted repeat regions (26,443 bp). In total, 129 genes were identified in Z. attopensis chloroplast genome, including 85 protein coding genes, eight rRNA, and 36 tRNA genes. Maximum-likelihood tree inferred from 58-gene sequences of 20 taxa supported that Rhamnaceae is sister to Elaeagnaceae and Z. attopensis is more closely related to Ziziphus jujuba.

Genome Characterization, Comparison and Phylogenetic Analysis of Complete Mitochondrial Genome of Evolvulus alsinoides Reveals Highly Rearranged Gene Order in Solanales

Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A's and G's in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.

Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny

Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.

Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species

In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.

Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689-150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796-82,919 bp), a small single copy region (SSC, 17,084-17,092 bp), and a pair of inverted repeat regions (IRs, 25,401-25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%-38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid

Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.

Dates and rates in grape's plastomes: evolution in slow motion

The family Vitaceae includes the domesticated grapevine (Vitis vinifera), one of the most economically important crops in the world. Despite the importance of Vitaceae, there is still considerable controversy surrounding their phylogenetic relationships and evolutionary timescales. Moreover, variation in rates of molecular evolution among Vitaceae remains mostly unexplored. The present research aims to fill these knowledge gaps through the analysis of plastome sequences. Thirteen newly sequenced grape plastomes are presented and their phylogenetic relationships examined. Divergence times and absolute substitution rates are inferred under different molecular clocks by the analysis of 95 non-coding plastid regions and 43 representative accessions of the major lineages of Vitaceae. Furthermore, the phylogenetic informativeness of non-coding plastid regions is investigated. We find strong evidence in favor of the random local clock model and rate heterogeneity within Vitaceae. Substitution rates decelerate in Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, and Vitis, with genus Vitis showing the lowest values up to a minimum of ~ 4.65 × 10^-11 s/s/y. We suggest that liana-like species of Vitaceae evolve slower than erect growth habit plants and we invoke the "rate of mitosis hypothesis" to explain the observed pattern of the substitution rates. We identify a reduced set of 20 non-coding regions able to accurately reconstruct the phylogeny of Vitaceae and we provide a detailed description of all 152 non-coding regions identified in the plastomes of subg. Vitis. These polymorphic regions will find their applications in phylogenetics, phylogeography, and population genetics as well in grapes identification through DNA barcoding techniques.

The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species

Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

The complete chloroplast genome sequence of Berchemia berchemiifolia (Rhamnaceae)

The complete chloroplast genome sequence of Berchemia berchemiifolia, rare plant to Korea, was determined in this study. The total genome size was 160,410 bp in length, containing a pair of inverted repeats (IRs) of 26,514 bp, which were separated by a large single copy (LSC) and small single copy (SSC) of 88,627 bp and 18,755 bp, respectively. The overall GC contents of the chloroplast genome were 37.2%. One hundred twenty nine genes were annotated, including 84 protein coding genes, 37 tRNA genes, and 8 rRNA genes. In these genes, 18 genes contained one or two introns. The phylogenetic tree showed that Berchemia berchemiifolia was most closely related to Berchemiella wilsonii.

Organellar genome assembly methods and comparative analysis of horticultural plants

Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows-Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.

The complete genome of Ziziphus jujuba cv. dongzao, an economic crop in Yellow River Delta of China

The complete chloroplast genome of Ziziphus jujuba cv. dongzao, known as an important economic cultivar in Yellow River Delta of China was reported. It exhibits a quadripartite structure with 161,493 bp including a large single copy region (89,178 bp), a small single copy region (19,357 bp) and a pair of inverted repeats regions (26,479 bp). It has 36.79% GC content and 114 unique genes. Phylogenetic analysis showed that it was a member of Ziziphus and more closely related to Berchemiella wilsonii. Border analysis revealed that there were some differences in the borders of the four related cultivars.

The complete chloroplast genome sequence of an economic plant Coffea canephora

Coffea canephora is a paramount economic plant with great economic value. The complete chloroplast (cp) genome is 154,751 bp in length, including a large single copy (LSC) region of 84,850 bp, a small single copy (SSC) region of 18,131 bp and a pair of inverted repeats (IRs) of 25,885bp. This cp genome contains 131 genes, comprising of 86 protein-coding genes, 37 tRNAs and 8 rRNAs. The majority of these genes were single copy genes, while 18 genes existed as double copies, including 6 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7 and ycf2), 8 tRNA genes (trnA-UGC, trnG-GCC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC) and 4 rRNA genes (rrn4.5, rrn5, rrn16 and rrn23). A neighbour-joining phylogenetic tree was reconstructed to indicate that Coffea canephora is evolutionarily close to Olea europaea within Asterids. The complete cp genome will provide intragenic information for molecular phylogeny and biological studies of the Rubiales.