NONPHOTOSYNTHETIC METABOLISM IN PLASTIDS

The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species

The genus Aspidopterys has multiple functions in medicine, food and ecological restoration. Due to the similar morphological characteristics of some species and the limited genomic information hinder the studies on germplasm identification and molecular phylogeny analysis. In this study, we compared and explored the six complete chloroplast (cp) genomes including four Aspidopterys species (A. glabriuscula, A. concava, A. cavaleriei, A. obcordata), Banisteriopsis caapi and Bunchosia argentea. Their cp genomes in length were 158,473 to 161,091 bp, displaying the high conserved degree in the structure, gene arrangement and GC content. Moreover, 57-80 long repeats and 61-92 SSRs were identified, most of which were forward or palindromic repeats and mononucleotides, respectively. Eleven non-coding regions and 12 coding regions, especially ndhH_ndhA, rpl32_ndhF and ycf1, had the higher nucleotide diversity values that could can be regarded as DNA barcodes of Malpighiaceae species. In addition, the 9 genes (like accD, atpE, atpF, clpP) were conducted positive selection (Ka/Ks > 1). As indicated by phylogenetic analysis, those four Aspidopterys were clustered into single clade with other Malpighiaceae species and were closely related to B. caapi and B. argentea. This study sheds more lights on further phylogenetic, evolutionary and genetic diversity studies on the genus Aspidopterys and even the Malpighiaceae species.

Optimizing carbon and nitrogen metabolism in plants: From fundamental principles to practical applications

Carbon (C) and nitrogen (N) are fundamental elements essential for plant growth and development, serving as the structural and functional backbone of organic compounds and driving essential biological processes such as photosynthesis, carbohydrate metabolism, and N assimilation. The metabolism and transport of C involve the movement of sugars between shoots and roots through xylem and phloem transport systems, regulated by a sugar-signaling hub. Nitrogen uptake, transport, and metabolism are equally critical, with plants assimilating nitrate and ammonium through specialized transporters and enzymes in response to varying N levels to optimize growth and development. The coordination of C and N metabolism is key to plant productivity and the maintaining of agroecosystem stability. However, inefficient utilization of N fertilizers results in substantial environmental and economic challenges, emphasizing the urgent need to improve N use efficiency (NUE) in crops. Integrating efficient photosynthesis with N uptake offers opportunities for sustainable agricultural practices. This review discusses recent advances in understanding C and N transport, metabolism, and signaling in plants, with a particular emphasis on NUE-related genes in rice, and explores breeding strategies to enhance crop efficiency and agricultural sustainability.

Phylogeny and evolutionary dynamics of the Rubia genus based on the chloroplast genome of Rubia tibetica

Rubia tibetica, a well-known medicinal plant, holds significant medicinal value. In this study, we sequenced and assembled the complete chloroplast genome of R. tibetica and conducted comparative analyses with four other Rubia species to provide insights into genome structure, selective pressure, and phylogenetic relationships. The chloroplast genome of R. tibetica was 154,901 bp in length and exhibited a typical quadripartite circular structure. Comparative analysis revealed a highly conserved genome structure among Rubia species, with genome sizes ranging from 153,555 bp to 155,108 bp and a GC content of approximately 37%. Codon usage analysis indicated a preference for A/U-ending codons. Selective pressure analysis identified relaxed selection in genes such as rps15 and petA, suggesting species-specific adaptive strategies. Two hypervariable regions, rps16-trnQ and psaJ-rps18, were experimentally validated as potential molecular markers through PCR amplification and sequencing. However, sequencing results of the rps16-trnQ region differed from the reference chloroplast genome, requiring further investigation. Phylogenetic analysis was performed using maximum likelihood (ML) based on the complete chloroplast genome sequences of five Rubia species and confirmed the monophyly of the Rubia genus, with R. tibetica occupying a basal position. This suggesting the retention of ancestral traits and adaptation to the unique environment of the Qinghai-Tibet Plateau. Molecular dating analysis further revealed divergence times consistent with geological and climatic events in the region. These findings provide critical insights into the evolutionary dynamics of Rubia species and offer valuable resources for their classification, conservation, and medicinal application.

Chloroplast-nuclear genome interaction drives asymmetric inverted repeats in chloroplast genome of Huperzia

Huperzia plants are important natural medicine species that have attracted increased amounts of attention due to the presence of huperzine A (Hup A), which efficiently, selectively, and reversibly inhibits acetylcholinesterase activity. However, due to the complexity of the genome structure and lack of genetic information, the phylogenetic and evolutionary relationships of Huperzia species are still unclear. In this study, seven chloroplast genome structures of Huperzia were verified and comparatively analyzed, and the phylogenetic relationships between Huperzia and other related ferns were evaluated. The results showed that a 58 kb insertion in the middle of the IRb region in the seven chloroplast genomes led to large differences in sequence size, GC content and tRNA number between IRa and IRb. All seven chloroplast genomes exhibited asymmetric structural conformations in the IR regions. We used sequence alignment and screening of the organelle and nuclear genomes to identify the source of the gene. The inserted sequence had no homologous region with the mitochondrial genome, and the same sequence as another segment was found in the nuclear genome. Then, the chloroplast genomes of Huperzia were comparatively analyzed. Phylogenetic tree showed that Phlegmariurus and Huperzia were closely related and belonged to the same branch. H. javanica and Huperzia serrata are closely related. From the perspective of phylogenetic tree, their phylogenetic relationship is closely related to geographical distribution. In conclusion, this study provides insights into the interaction mechanism between chloroplast genome and nuclear genome and the phylogeny of Huperzia. In addition, by comparing the chloroplast genomes of Huperzia, we analyzed its genetic diversity and provided important molecular information for the protection of these endangered species.

Gibberellin biosynthesis gene ScGA20 oxidase enhances sugarcane growth by modulating genes associated with phytohormone and growth processes

Sugarcane is a globally significant crop for sugar and energy production, yet its breeding potential is limited by its complex genetic background and restricted genetic diversity. Molecular breeding presents a promising approach to boost sugarcane productivity. Gibberellins (GA) plays a critical role in plant growth and development, with GA20-oxidase being the most crucial enzyme in GA biosynthesis. In this study, we isolated the sugarcane gene encoding GA20-oxidase (ScGA20ox, OR283803) enzyme, a 43.88 kDa hydrophilic protein, and introduced it into sugarcane variety GT42 via biolistics transformation. Transgenic sugarcane expressing Ubi-driven ScGA20ox exhibited elevated GA levels and accelerated growth. Transcriptome analysis revealed that genes associated with plant hormone metabolism and growth-related pathways, including photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism were involved in the GA20ox-mediated growth in sugarcane. This work underscores the potential of GA20ox for enhancing sugarcane yields through transgenic approaches, while advancing our understanding of GA's regulatory role in the growth of this crucial sugar crop.

Comparative chloroplast genomes and phylogenetic analyses shed new insights on the phyloevolution of different ploidy in Camellia reticulata

BACKGROUND

Camellia reticulata Lindl. (C. reticulata) is the tallest ornamental camellia globally, with wild populations comprising a polyploid complex of diploids (2×), tetraploids (4×), and hexaploids (6×). The type specimen of C. reticulata is a heteroploid hexaploid derived from 2 × ancestors, including C. pitardii, C. saluenensis, and 2 × C. reticulata. Currently, limited information exists regarding the evolutionary characteristics of the chloroplast genomes of C. reticulata at different ploidy levels, and the phylogenetic position of 2 × and 4 × C. reticulata remains unclear.

RESULTS

This study sequenced, assembled, and annotated the chloroplast genomes of 2 × and 4 × C. reticulata, comparing them with those of 6 × C. reticulata and other closely related species. The results indicated that the chloroplast genome sizes of C. reticulata ranged from 156,519 to 156,927 bp, with gene counts, distributions, GC content, and codon usage being similar across different ploidy levels. The ycf1 gene exhibited significant differentiation among species, and was identified as a candidate for adaptive evolution in C. reticulata. Additionally, 11 highly differentiated intergenic regions were identified, with six hotspots of variation that can serve as molecular markers for genetic studies in C. reticulata populations. Analysis of selection pressure indicated that four genes were under positive selection. Phylogenetic analysis revealed that the polyploid complex of C. reticulata, along with C. pitardii, C. saluenensis, and C. mairei, formed a well-supported clade. The genetic distances between 6 × C. reticulata and its three 2 × ancestors were relatively small.

CONCLUSION

Camellia pitardii, C. saluenensis, and C. mairei may have participated in the allopolyploidization of C. reticulata, with both 2 × and 4 × C. reticulata have the potential for independent classification. These findings provide valuable insights into chloroplast genome alterations following allopolyploidization, establishing a crucial foundation for understanding the systematic evolutionary history of various ploidy levels in C. reticulata.

Interplay between tobacco curly shoot virus vsiRNA24 and triosephosphate isomerase: implications for Nicotiana benthamiana viral defense

Virus-derived small interfering RNAs (vsiRNAs) play an important role in viral infection by regulating the expression of host genes. At present, research on the regulation of plant primary metabolic pathways by vsiRNAs is very limited. TvsiRNA24 derived from tobacco curly shoot virus (TbCSV) was amplified by reverse transcription polymerase chain reaction, and its target gene NbTPI (triosephosphate isomerase) was verified using reverse transcription quantitative polymerase chain reaction and GFP fluorescence observation. The effect of the interaction between TvsiRNA24 and NbTPI on TbCSV infection was analyzed by virus mediated, genetic transformation, western blotting, and quantitative detection. The expression of TvsiRNA24 retards the growth of Nicotiana benthamiana and enhances TbCSV accumulation within N. benthamiana. The overexpression of NbTPI attenuates the accumulation of TbCSV, and the silencing of NbTPI leads to the growth retardation of N. benthamiana and intensifies symptoms post-TbCSV infection. Moreover, the expression of some genes related to photosynthesis, primary metabolism and immune response is regulated by NbTPI. Our results unveil the specific role of TvsiRNA24-NbTPI in the pathogenicity of TbCSV, resulting in hindrance to plant growth and facilitation of viral infection. The identification of this regulatory pathway provides valuable insights that can be utilized to devise novel antiviral approaches targeting the reduction of viral pathogenicity.

The evolution of the plastid genomes in the holoparasitic Balanophoraceae

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions in their plastomes. The characteristics of the minimum plastome required for survival, if they exist, remain a topic of debate. The holoparasitic family Balanophoraceae was initially presumed to have entirely lost their plastids, however, recent reports revealed the presence of reduced and aberrant plastids with odd genomes. Among the outstanding features of these genomes are the highest nucleotide composition bias across the tree of life and the only two genetic code changes ever recorded among plants. In this study, we assembled the plastomes from five genera, four of which had never been studied. Major common features include extremely high AT content, the lack of a typical quadripartite structure and extensive size reduction due to gene elimination and genome compaction. The family exhibits multiple gene and intron losses, and a broad range of scenarios regarding the evolution of the plastid trnE, a gene considered essential because of its dual function in tetrapyrrole biosynthesis and translation within the plastid. In addition, phylogenetic analyses suggest that the genus Scybalium is not monophyletic. An evolutionary model for the plastomes of the Balanophoraceae is proposed.

Complete mitogenome characteristics and phylogenetic analysis of traditional Chinese medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family

BACKGROUND

Tinospora sagittata, a member belongs to the genus Tinospora of Menispermaceae family. Its tuberous roots have been used as traditional Chinese medicine (TCM) for pharmacological properties and are commonly known name as "Jin Guo Lan". Although its plastome and nuclear genome had been sequenced, its mitochondrial genome has not been explored, which significantly hampers conservation efforts and further research for this species. In addition, previous efforts based on multiple molecular markers providing profound insights into an intergeneric phylogenetic framework for Burasaieae and sampled species of T. sagittata are placed in a superclades, species delimitation of T. sagittata still need to be comprehensively evaluated.

RESULTS

Flow cytometry revealed that Tinospora sagittata has two cytotypes and a wide range in genome sizes. We further sequenced and assembled the organelle genomes of T. sagittata, including the mitogenome (513,210-513,215 bp) and plastome (163,621-164,006 bp). The plastomes were highly similar in gene content and exhibited a typical quadripartite structure, but a translocation as well as two inversions were detected in mitogenomes. The repeats patterns in both organelles are generally similar, but significant difference in the codon bias of the genes of Tinospora organelle genomes. Interesting, both organelle genomes had shown that inter-gene spacer regions could be used as effective molecular markers for further phylogenetic analyses and species identification. Comprehensive analysis of protein coding genes of organelle genomes showed that significant difference in Ka, Ks, and Ka/Ks values among the organelle genomes. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Ranunculales described in the APG IV system.

CONCLUSIONS

We provided a high-quality and well-annotated organelle genome for Tinospora sagittata. The study present here advances our understanding of the intricate interplay between plastome and mitogenome. Moreover, our results also laid the foundation for further studying the course, tempo and mode of organelle genome evolution of Menispermaceae.

Comparative and Adaptive Analyses of the Complete Chloroplast Genome Diversity in Sium serra

BACKGROUND/OBJECTIVES

Sium serra is distributed in Korea, China, and Japan. It was first identified as the genus Pimpinella and then reclassified as Sium by Kitagawa. Some Sium species are used as herbal medicine and are often confused with the similar form Ligusticum sinense. In this study, we analyzed the cp genome of S. serra and conducted comparative analyses with the cp genomes of related taxa.

METHODS

We extracted gDNA from fresh leaves and sequenced it using Illumina HiSeq2500. For the chloroplast genome assembly, de novo assembly was performed using Velvet v1.2.07. For the annotation, GeSeq and NCBI BLASTN were used. Afterwards, related taxa were analyzed using programs such as DnaSP and MISA.

RESULTS

S. serra was excluded from the study on the chloroplast (cp) genome in Sium because it was classified as Pimpinella in China. Therefore, this study aimed to analyze the cp genome of S. serra for the first time and its location within the genus Sium. The complete cp genome of S. serra was 154,755 bp in length, including a pair of inverted repeats, each 26,255 bp, a large single-copy region of 84,581 bp, and a small single-copy region of 17,664 bp. The cp genome comprised 79 protein-coding, 30 tRNA, and 4 rRNA genes. Furthermore, six regions of high nucleotide diversity were identified in the genus Sium. In the genus Sium, 1630 repeats that can serve as markers were also identified. Eight protein-coding genes with high KA/KS values were under positive selection in the Sium. Our phylogenetic analyses suggest that S. serra was positioned with high bootstrap support within the Sium of the tribe Oenantheae, specifically in the southern Palearctic subclade.

CONCLUSIONS

In this study, the S. serra chloroplast genome was sequenced and assembled. The genus Sium formed a monophyletic group; however, as not all the Sium species were included in this study, further research is necessary. This study can serve as foundational data not only for Sium but also for the tribe Oenantheae.

Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant

Cinnamomum daphnoides (Siebold & Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species' chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species' cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.

Physiological and Transcriptome Analyses Provide Insights into the Response of Grain Filling to High Temperature in Male-Sterile Wheat (Triticum aestivum L.) Lines

High-temperature (HT) stress frequently affects the early and middle stages of grain filling in hybrid seed production regions. Photo-thermo-sensitive male-sterile (PTMS) wheat lines, which play a critical role as female parents in hybrid seed production, face challenges under HT conditions. However, the mechanisms governing grain filling in PTMS lines under HT stress remain poorly understood. This study used the BS253 line to investigate the effects of HT on grain filling, primarily focusing on the transition from sucrose unloading to starch synthesis. The findings indicated that HT significantly reduced the grain starch content and weight by 7.65% and 36.35% at maturity, respectively. Further analysis revealed that the expression levels of TaSUT1 and TaSWEETs in grains initially increased after HT stress, paralleling the rise in sucrose content during the same period. The activities of ADP-glucose pyrophosphorylase, UDP-glucose pyrophosphorylase, granule-bound starch synthase, and soluble starch synthase were markedly decreased, indicating that impaired starch synthesis was a key factor limiting grain filling immediately after HT exposure. A total of 41 key regulatory genes involved in sucrose-to-starch metabolism were identified, with HT significantly reducing the expression of genes associated with pathways from sucrose unloading to starch synthesis during the middle and late stages post-HT. Based on the observed ultrastructural changes in the abdominal phloem and sucrose transporter expression levels under HT, we concluded that limited sucrose supply, degradation, and inhibition of starch synthesis collectively constrained grain filling during these stages. Additionally, 11 heat shock proteins and two catalase genes were identified and significantly upregulated during the initial phase post-HT, suggesting their potential role in enhancing sucrose supply at this critical time. More importantly, seven key genes involved in the sucrose-to-starch pathway were identified by weighted gene co-expression network analysis (WGCNA), which provides target genes for their functional research for starch synthase. These findings provide a comprehensive understanding of how HT limits grain filling, identify several genes involved in the sucrose-to-starch pathway, and offer a novel perspective for future research on HT-restricted grain filling across the entire process from sucrose unloading to starch synthesis in developing grains.

Chlorophyll and Carotenoid Metabolism Varies with Growth Temperatures among Tea Genotypes with Different Leaf Colors in Camellia sinensis

The phenotype of albino tea plants (ATPs) is significantly influenced by temperature regimes and light conditions, which alter certain components of the tea leaves leading to corresponding phenotypic changes. However, the regulatory mechanism of temperature-dependent changes in photosynthetic pigment contents and the resultant leaf colors remain unclear. Here, we examined the chloroplast microstructure, shoot phenotype, photosynthetic pigment content, and the expression of pigment synthesis-related genes in three tea genotypes with different leaf colors under different temperature conditions. The electron microscopy results revealed that all varieties experienced the most severe chloroplast damage at 15 °C, particularly in albino cultivar Baiye 1 (BY), where chloroplast basal lamellae were loosely arranged, and some chloroplasts were even empty. In contrast, the chloroplast basal lamellae at 35 °C and 25 °C were neatly arranged and well-developed, outperforming those observed at 20 °C and 15 °C. Chlorophyll and carotenoid measurements revealed a significant reduction in chlorophyll content under low temperature treatment, peaking at ambient temperature followed by high temperatures. Interestingly, BY showed remarkable tolerance to high temperatures, maintaining relatively high chlorophyll content, indicating its sensitivity primarily to low temperatures. Furthermore, the trends in gene expression related to chlorophyll and carotenoid metabolism were largely consistent with the pigment content. Correlation analysis identified key genes responsible for temperature-induced changes in these pigments, suggesting that changes in their expression likely contribute to temperature-dependent leaf color variations.

Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties of Vitis vinifera from the Don Valley

The autochthonous grape varieties of the Don Valley, situated in southern Russia, constitute a distinctive element of regional cultural heritage. These varieties have been adapted over centuries to the region's specific local climatic and soil conditions. For the most part, these varieties are not imported from other countries. They are closely related to varieties found in Crimea and the North Caucasus. In this study, we obtained the first complete, unfragmented sequences of the chloroplast genomes of eight autochthonous varieties from the Don Valley and one from Crimea. We also performed a comparative analysis of their genomic features. The size of Vitis vinifera chloroplast genome sequences varied from 160,925 to 160,991 bp, depending on the cultivar, with a uniform GC ratio of 37.38%. Each genome consists of four subregions: a single copy region (LSC) ranging from 89,158 to 89,336 bp, a small single copy region (SSC) ranging from 19,070 to 19,073 bp, and a pair of inverted repeat regions (IRa and IRb) in the range of 26,292 to 26,353 bp. The chloroplast genomes of the studied V. vinifera varieties contained 130 genes, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The sequence divergence analysis has enabled the identification of four highly variable regions, which may be utilized as potential markers for phylogenetic analysis. The analysis revealed the presence of 58 to 61 SSRs and multiple long repeated sequences in the chloroplast genomes of these varieties. The phylogenetic analyses of the sequences obtained and complete chloroplast genomes available from public databases indicated that the majority of autochthonous V. vinifera varieties do not have a direct origin from any European variety.

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

Redox regulation in chloroplast thylakoid lumen: The pmf changes everything, again

Photosynthesis is the foundation of life on Earth. However, if not well regulated, it can also generate excessive reactive oxygen species (ROS), which can cause photodamage. Regulation of photosynthesis is highly dynamic, responding to both environmental and metabolic cues, and occurs at many levels, from light capture to energy storage and metabolic processes. One general mechanism of regulation involves the reversible oxidation and reduction of protein thiol groups, which can affect the activity of enzymes and the stability of proteins. Such redox regulation has been well studied in stromal enzymes, but more recently, evidence has emerged of redox control of thylakoid lumenal enzymes. This review/hypothesis paper summarizes the latest research and discusses several open questions and challenges to achieving effective redox control in the lumen, focusing on the distinct environments and regulatory components of the thylakoid lumen, including the need to transport electrons across the thylakoid membrane, the effects of pH changes by the proton motive force (pmf) in the stromal and lumenal compartments, and the observed differences in redox states. These constraints suggest that activated oxygen species are likely to be major regulatory contributors to lumenal thiol redox regulation, with key components and processes yet to be discovered.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species

Bromus (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced Bromus ciliatus, Bromus benekenii, Bromus riparius, and Bromus rubens chloroplast genomes and compared them with four previously described species. The genome sizes of Bromus species ranged from 136,934 bp (Bromus vulgaris) to 137,189 bp (Bromus ciliates, Bromus biebersteinii), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that Bromus is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of Bromus provides a scientific basis for species identification and phylogenetic studies.

Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis

The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.

Light-independent pathway of STN7 kinase activation under low temperature stress in runner bean (Phaseolus coccineus L.)

BACKGROUND

The phosphorylation of the Light-Harvesting Complex of photosystem II (LHCII) driven by STATE TRANSITION 7 (STN7) kinase is a part of one of the crucial regulatory mechanisms of photosynthetic light reactions operating in fluctuating environmental conditions, light in particular. There are evidenced that STN7 can also be activated without light as well as in dark-chilling conditions. However, the biochemical mechanism standing behind this complex metabolic pathway has not been deciphered yet.

RESULTS

In this work, we showed that dark-chilling induces light-independent LHCII phosphorylation in runner bean (Phaseolus coccineus L.). In dark-chilling conditions, we registered an increased reduction of the PQ pool which led to activation of STN7 kinase, subsequent LHCII phosphorylation, and possible LHCII relocation inside the thylakoid membrane. We also presented the formation of a complex composed of phosphorylated LHCII and photosystem I typically formed upon light-induced phosphorylation. Moreover, we indicated that the observed steps were preceded by the activation of the oxidative pentose phosphate pathway (OPPP) enzymes and starch accumulation.

CONCLUSIONS

Our results suggest a direct connection between photosynthetic complexes reorganization and dark-chilling-induced activation of the thioredoxin system. The proposed possible pathway starts from the activation of OPPP enzymes and further NADPH-dependent thioredoxin reductase C (NTRC) activation. In the next steps, NTRC simultaneously activates ADP-glucose pyrophosphorylase and thylakoid membrane-located NAD(P)H dehydrogenase-like complex. These results in starch synthesis and electron transfer to the plastoquinone (PQ) pool, respectively. Reduced PQ pool activates STN7 kinase which phosphorylates LHCII. In this work, we present a new perspective on the mechanisms involving photosynthetic complexes while efficiently operating in the darkness. Although we describe the studied pathway in detail, taking into account also the time course of the following steps, the biological significance of this phenomenon remains puzzling.

Transcriptional and post-transcriptional regulation of chloroplast development by nuclear-localized XAP5 CIRCADIAN TIMEKEEPER

Chlorophyll biosynthesis and breakdown, important cellular processes for photosynthesis, occur in the chloroplast. As a semi-autonomous organelle, chloroplast development is mainly regulated by nuclear-encoded chloroplast proteins and proteins encoded by itself. However, the knowledge of chloroplast development regulated by other organelles is limited. Here, we report that the nuclear-localized XAP5 CIRCADIAN TIMEKEEPER (XCT) is essential for chloroplast development in Arabidopsis. In this study, significantly decreased chlorophyll content phenotypes of cotyledons and subsequently emerging organs from shoot apical meristem were observed in xct-2. XCT is constitutively expressed in various tissues and localized in the nuclear with speckle patterns. RNA-seq analysis identified 207 differently spliced genes and 1511 differently expressed genes, in which chloroplast development-, chlorophyll metabolism- and photosynthesis-related genes were enriched. Further biochemical assays suggested that XCT was co-purified with the well-known splicing factors and transcription machinery, suggesting dual functions of XCT in gene transcription and splicing. Interestingly, we also found that the chlorophyll contents in xct-2 significantly decreased under high temperature and high light condition, indicating XCT integrates temperature and light signals to fine-tune the chlorophyll metabolism in Arabidopsis. Therefore, our results provide new insights into chloroplast development regulation by XCT, a nuclear-localized protein, at the transcriptional and post-transcriptional level.

Comparative and phylogenetic analyses of Loranthaceae plastomes provide insights into the evolutionary trajectories of plastome degradation in hemiparasitic plants

BACKGROUND

The lifestyle transition from autotrophy to heterotrophy often leads to extensive degradation of plastomes in parasitic plants, while the evolutionary trajectories of plastome degradation associated with parasitism in hemiparasitic plants remain poorly understood. In this study, phylogeny-oriented comparative analyses were conducted to investigate whether obligate Loranthaceae stem-parasites experienced higher degrees of plastome degradation than closely related facultative root-parasites and to explore the potential evolutionary events that triggered the 'domino effect' in plastome degradation of hemiparasitic plants.

RESULTS

Through phylogeny-oriented comparative analyses, the results indicate that Loranthaceae hemiparasites have undergone varying degrees of plastome degradation as they evolved towards a heterotrophic lifestyle. Compared to closely related facultative root-parasites, all obligate stem-parasites exhibited an elevated degree plastome degradation, characterized by increased downsizing, gene loss, and pseudogenization, thereby providing empirical evidence supporting the theoretical expectation that evolution from facultative parasitism to obligate parasitism may result in a higher degree of plastome degradation in hemiparasites. Along with infra-familial divergence in Loranthaceae, several lineage-specific gene loss/pseudogenization events occurred at deep nodes, whereas further independent gene loss/pseudogenization events were observed in shallow branches.

CONCLUSIONS

The findings suggest that in addition to the increasing levels of nutritional reliance on host plants, cladogenesis can be considered as another pivotal evolutionary event triggering the 'domino effect' in plastome degradation of hemiparasitic plants. These findings provide new insights into the evolutionary trajectory of plastome degradation in hemiparasitic plants.

Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops

BACKGROUND

Plants differ more than threefold in seed oil contents (SOCs). Soybean (Glycine max), cotton (Gossypium hirsutum), rapeseed (Brassica napus), and sesame (Sesamum indicum) are four important oil crops with markedly different SOCs and fatty acid compositions.

RESULTS

Compared to grain crops like maize and rice, expanded acyl-lipid metabolism genes and relatively higher expression levels of genes involved in seed oil synthesis (SOS) in the oil crops contributed to the oil accumulation in seeds. Here, we conducted comparative transcriptomics on oil crops with two different SOC materials. In common, DIHYDROLIPOAMIDE DEHYDROGENASE, STEAROYL-ACYL CARRIER PROTEIN DESATURASE, PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE, and oil-body protein genes were both differentially expressed between the high- and low-oil materials of each crop. By comparing functional components of SOS networks, we found that the strong correlations between genes in "glycolysis/gluconeogenesis" and "fatty acid synthesis" were conserved in both grain and oil crops, with PYRUVATE KINASE being the common factor affecting starch and lipid accumulation. Network alignment also found a conserved clique among oil crops affecting seed oil accumulation, which has been validated in Arabidopsis. Differently, secondary and protein metabolism affected oil synthesis to different degrees in different crops, and high SOC was due to less competition of the same precursors. The comparison of Arabidopsis mutants and wild type showed that CINNAMYL ALCOHOL DEHYDROGENASE 9, the conserved regulator we identified, was a factor resulting in different relative contents of lignins to oil in seeds. The interconnection of lipids and proteins was common but in different ways among crops, which partly led to differential oil production.

CONCLUSIONS

This study goes beyond the observations made in studies of individual species to provide new insights into which genes and networks may be fundamental to seed oil accumulation from a multispecies perspective.

Starch and sucrose metabolism plays an important role in the stem development in Medicago sativa

The forage quality of alfalfa (Medicago sativa ) stems is greater than the leaves. Sucrose hydrolysis provides energy for stem development, with starch being enzymatically converted into sucrose to maintain energy homeostasis. To understand the physiological and molecular networks controlling stem development, morphological characteristics and transcriptome profiles in the stems of two alfalfa cultivars (Zhungeer and WL168) were investigated. Based on transcriptome data, we analysed starch and sugar contents, and enzyme activity related to starch-sugar interconversion. Zhungeer stems were shorter and sturdier than WL168, resulting in significantly higher mechanical strength. Transcriptome analysis showed that starch and sucrose metabolism were significant enriched in the differentially expressed genes of stems development in both cultivars. Genes encoding INV , bglX , HK , TPS and glgC downregulated with the development of stems, while the gene encoding was AMY upregulated. Weighted gene co-expression network analysis revealed that the gene encoding glgC was pivotal in determining the variations in starch and sucrose contents between the two cultivars. Soluble carbohydrate, sucrose, and starch content of WL168 were higher than Zhungeer. Enzyme activities related to sucrose synthesis and hydrolysis (INV, bglX, HK, TPS) showed a downward trend. The change trend of enzyme activity was consistent with gene expression. WL168 stems had higher carbohydrate content than Zhungeer, which accounted for more rapid growth and taller plants. WL168 formed hollow stems were formed during rapid growth, which may be related to the redistribution of carbohydrates in the pith tissue. These results indicated that starch and sucrose metabolism play important roles in the stem development in alfalfa.

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis

Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.

Sensitivity and responses of chloroplasts to salt stress in plants

Chloroplast, the site for photosynthesis and various biochemical reactions, is subject to many environmental stresses including salt stress, which affects chloroplast structure, photosynthetic processes, osmotic balance, ROS homeostasis, and so on. The maintenance of normal chloroplast function is essential for the survival of plants. Plants have developed different mechanisms to cope with salt-induced toxicity on chloroplasts to ensure the normal function of chloroplasts. The salt tolerance mechanism is complex and varies with plant species, so many aspects of these mechanisms are not entirely clear yet. In this review, we explore the effect of salinity on chloroplast structure and function, and discuss the adaptive mechanisms by which chloroplasts respond to salt stress. Understanding the sensitivity and responses of chloroplasts to salt stress will help us understand the important role of chloroplasts in plant salt stress adaptation and lay the foundation for enhancing plant salt tolerance.

The kiwifruit amyloplast proteome (kfALP): a resource to better understand the mechanisms underlying amyloplast biogenesis and differentiation

The biogenesis and differentiation (B&D) of amyloplasts contributes to fruit flavor and color. Here, remodeling of starch granules, thylakoids and plastoglobules was observed during development and ripening in two kiwifruit (Actinidia spp.) cultivars - yellow-fleshed 'Hort16A' and green-fleshed 'Hayward'. A protocol was developed to purify starch-containing plastids with a high degree of intactness, and amyloplast B&D was studied using label-free-based quantitative proteomic analyses in both cultivars. Over 3000 amyloplast-localized proteins were identified, of which >98% were quantified and defined as the kfALP (kiwifruit amyloplast proteome). The kfALP data were validated by Tandem-Mass-Tag (TMT) labeled proteomics in 'Hort16A'. Analysis of the proteomic data across development and ripening revealed: 1) a conserved increase in the abundance of proteins participating in starch synthesis/degradation during both amyloplast B&D; 2) up-regulation of proteins for chlorophyll degradation and of plastoglobule-localized proteins associated with chloroplast breakdown and plastoglobule formation during amyloplast differentiation; 3) constitutive expression of proteins involved in ATP supply and protein import during amyloplast B&D. Interestingly, two different pathways of amyloplast B&D were observed in the two cultivars. In 'Hayward', significant increases in abundance of photosynthetic- and tetrapyrrole metabolism-related proteins were observed, but the opposite trend was observed in 'Hort16A'. In conclusion, analysis of the kfALP provides new insights into the potential mechanisms underlying amyloplast B&D with relevance to key fruit quality traits in contrasting kiwifruit cultivars.

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.

Chloroplast genome analyses of Caragana arborescens and Caragana opulens

BACKGROUND

Numerous species within the genus Caragana have high ecological and medicinal value. However, species identification based on morphological characteristics is quite complicated in the genus. To address this issue, we analyzed complete plastid genome data for the genus.

RESULTS

We obtained chloroplast genomes of two species, Caragana arborescens and Caragana opulens, using Illumina sequencing technology, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species indicated that they could be assigned to the inverted repeat-lacking clade (IRLC). The genomes included 111 distinct genes (4 rRNA genes, 31 tRNA genes, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in the two genomes, the majority of which contained a single intron. Repeat analyses revealed 129 and 229 repeats in C. arborescens and C. opulens, respectively. C. arborescens and C. opulens genomes contained 277 and 265 simple sequence repeats, respectively. The two Caragana species exhibited similar codon usage patterns. rpl20-clpP, rps19-rpl2, and rpl23-ycf2 showed the highest nucleotide diversity (pi). In an analysis of sequence divergence, certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) were highly variable. A phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together with four other Caragana species. The genera Astragalus and Caragana were relatively closely related.

CONCLUSIONS

The present study provides valuable information about the chloroplast genomes of C. arborescens and C. opulens and lays a foundation for future phylogenetic research and molecular marker development.

Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China

Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.

Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa

Alfalfa (Medicago sativa) is a perennial forage legume that is widely distributed all over the world; therefore, it has an extremely complex genetic background. Though population structure and phylogenetic studies have been conducted on a large group of alfalfa nuclear genomes, information about the chloroplast genomes is still lacking. Chloroplast genomes are generally considered to be conservative and play an important role in population diversity analysis and species adaptation in plants. Here, 231 complete alfalfa chloroplast genomes were successfully assembled from 359 alfalfa resequencing data, on the basis of which the alfalfa chloroplast pan-genome was constructed. We investigated the genetic variations of the alfalfa chloroplast genome through comparative genomic, genetic diversity, phylogenetic, population genetic structure, and haplotype analysis. Meanwhile, the expression of alfalfa chloroplast genes under cold stress was explored through transcriptome analysis. As a result, chloroplast genomes of 231 alfalfa lack an IR region, and the size of the chloroplast genome ranges from 125,192 bp to 126,105 bp. Using population structure, haplotypes, and construction of a phylogenetic tree, it was found that alfalfa populations could be divided into four groups, and multiple highly variable regions were found in the alfalfa chloroplast genome. Transcriptome analysis showed that tRNA genes were significantly up-regulated in the cold-sensitive varieties, while rps7, rpl32, and ndhB were down-regulated, and the editing efficiency of ycf1, ycf2, and ndhF was decreased in the cold-tolerant varieties, which may be due to the fact that chloroplasts store nutrients through photosynthesis to resist cold. The huge number of genetic variants in this study provide powerful resources for molecular markers.

The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato

In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.

Chloroplast genome of Justicia procumbens: genomic features, comparative analysis, and phylogenetic relationships among Justicieae species

Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454 bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.

Coordinated Transcriptome and Metabolome Analyses of a Barley hvhggt Mutant Reveal a Critical Role of Tocotrienols in Endosperm Starch Accumulation

Tocotrienols and tocopherols (vitamin E) are potent antioxidants that are synthesized in green plants. Unlike ubiquitous tocopherols, tocotrienols predominantly accumulate in the endosperm of monocot grains, catalyzed by homogentiate geranylgeranyl transferase (HGGT). Previously, we generated a tocotrienol-deficient hvhggt mutant with shrunken barley grains. However, the relationship between tocotrienols and grain development remains unclear. Here, we found that the hvhggt lines displayed hollow endosperms with defective transfer cells and reduced aleurone layers. The carbohydrate and starch contents of the hvhggt endosperm decreased by approximately 20 and 23%, respectively. Weighted gene coexpression network analyses identified a critical gene module containing HvHGGT, which was strongly associated with the hvhggt mutation and enriched with gene functions in starch and sucrose metabolism. Metabolome measurements revealed an elevated soluble sugar content in the hvhggt endosperm, which was significantly associated with the identified gene modules. The hvhggt endosperm had significantly higher NAD(H) and NADP(H) contents and lower levels of ADPGlc (regulated by redox balance) than the wild-type, consistent with the absence of tocotrienols. Interestingly, exogenous α-tocotrienol spraying on developing hvhggt spikes partially rescued starch accumulation and endosperm defects. Our study supports a potential novel function of tocotrienols in grain starch accumulation and endosperm development in monocot crops.

An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae)

Abstract We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.

The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications

Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.

Loss of plastid ndh genes in an autotrophic desert plant

Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.

Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth

In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.

Comparative Analysis of the Chloroplast Genome of Sicyos angulatus with Other Seven Species of Cucurbitaceae Family

Sicyos angulatus (SA) is an annual plant from the Cucurbitaceae family that is native to the eastern part of North America. This study aims to assemble and annotate the chloroplast genome of S. angulatus, and then compare it with plastomes of the other species representing the Cucurbitaceae family. The chloroplast genome size of S. angulatus is 154,986 bp, including a pair of inverted repeats (IR) of 26,276 bp, and small single-copy region (SSC) of 18,079 bp and large single-copy region (LSC) of 84,355 bp. Compared to other Cucurbitaceae species, the chloroplast genome of S. angulatus is almost 4222 bp smaller than the plastome Gynostemma pentaphyllum. All other seven species have an identical set of tRNA (37), except Citrullus laevigata, which contains 36 tRNA. The IRa/LSC junction in all eight species is located upstream of rpl2 and downstream of trnH gene. Moreover, variation in the size of the gene and the presence of pseudogene ycf1 has been seen because of the IR contraction and expansion. The highest number of tandem repeats was seen in G. pentaphyllum, and then Corynocarpus leavigata. The sequence divergence analysis and topology of the phylogenetic tree indicate that S. angulatus is more similar to genus Citrullus as compared to genus Gynostemma. These findings contribute to developing the genomic marker for the purpose of future genetic studies.

Iron uptake of etioplasts is independent from photosynthesis but applies the reduction-based strategy

Introduction

Iron (Fe) is one of themost important cofactors in the photosynthetic apparatus, and its uptake by chloroplasts has also been associated with the operation of the photosynthetic electron transport chain during reduction-based plastidial Fe uptake. Therefore, plastidial Fe uptake was considered not to be operational in the absence of the photosynthetic activity. Nevertheless, Fe is also required for enzymatic functions unrelated to photosynthesis, highlighting the importance of Fe acquisition by non-photosynthetic plastids. Yet, it remains unclear how these plastids acquire Fe in the absence of photosynthetic function. Furthermore, plastids of etiolated tissues should already possess the ability to acquire Fe, since the biosynthesis of thylakoid membrane complexes requires a massive amount of readily available Fe. Thus, we aimed to investigate whether the reduction-based plastidial Fe uptake solely relies on the functioning photosynthetic apparatus.

Methods

In our combined structure, iron content and transcript amount analysis studies, we used Savoy cabbage plant as a model, which develops natural etiolation in the inner leaves of the heads due to the shading of the outer leaf layers.

Results

Foliar and plastidial Fe content of Savoy cabbage leaves decreased towards the inner leaf layers. The leaves of the innermost leaf layers proved to be etiolated, containing etioplasts that lacked the photosynthetic machinery and thus were photosynthetically inactive. However, we discovered that these etioplasts contained, and were able to take up, Fe. Although the relative transcript abundance of genes associated with plastidial Fe uptake and homeostasis decreased towards the inner leaf layers, both ferric chelate reductase FRO7 transcripts and activity were detected in the innermost leaf layer. Additionally, a significant NADP(H) pool and NAD(P)H dehydrogenase activity was detected in the etioplasts of the innermost leaf layer, indicating the presence of the reducing capacity that likely supports the reduction-based Fe uptake of etioplasts.

Discussion

Based on these findings, the reduction-based plastidial Fe acquisition should not be considered exclusively dependent on the photosynthetic functions.

Variation in Rice Plastid Genomes in Wide Crossing Reveals Dynamic Nucleo-Cytoplasmic Interaction

Plastid genomes (plastomes) of angiosperms are well known for their relative stability in size, structure, and gene content. However, little is known about their heredity and variations in wide crossing. To such an end, the plastomes of five representative rice backcross inbred lines (BILs) developed from crosses of O. glaberrima/O. sativa were analyzed. We found that the size of all plastomes was about 134,580 bp, with a quadripartite structure that included a pair of inverted repeat (IR) regions, a small single-copy (SSC) region and a large single-copy (LSC) region. They contained 76 protein genes, 4 rRNA genes, and 30 tRNA genes. Although their size, structure, and gene content were stable, repeat-mediated recombination, gene expression, and RNA editing were extensively changed between the maternal line and the BILs. These novel discoveries demonstrate that wide crossing causes not only nuclear genomic recombination, but also plastome variation in plants, and that the plastome plays a critical role in coordinating the nuclear-cytoplasmic interaction.

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles

The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, classification, conserved motifs, cis-elements, chromosomal locations, evolution and expression patterns of the PtGLK genes in the woody model plant Populus trichocarpa were analyzed in detail. In total, 55 putative PtGLKs (PtGLK1-PtGLK55) were identified and divided into 11 distinct subfamilies according to the gene structure, motif composition and phylogenetic analysis. Synteny analysis showed that 22 orthologous pairs and highly conservation between regions of GLK genes across P. trichocarpa and Arabidopsis were identified. Furthermore, analysis of the duplication events and divergence times provided insight into the evolutionary patterns of GLK genes. The previously published transcriptome data indicated that PtGLK genes exhibited distinct expression patterns in various tissues and different stages. Additionally, several PtGLKs were significantly upregulated under the responses of cold stress, osmotic stress, and methyl jasmonate (MeJA) and gibberellic acid (GA) treatments, implying that they might take part in abiotic stress and phytohormone responses. Overall, our results provide comprehensive information on the PtGLK gene family and elucidate the potential functional characterization of PtGLK genes in P. trichocarpa.

The first chloroplast sequence of Rosa davurica Pall. var. Davurica

Rosa davurica Pall. var. davurica is a member of the plant family Rosaceae. Although R. davurica has high application value, its chloroplast genome sequence has not been reported. This study aims to reveal the genetic characteristics of the chloroplast genome of Rosa roxburghii. The length of its total chloroplast DNA is 156,971 bp, with 37.22% G/C content. Its chloroplast genome has two inverted repeat (IRa and IRb) regions totaling 26,051 bp which are separated by a large single copy (LSC) region of 86,032 bp and a small single copy (SSC) region of 18,837 bp. The genome contains 131 independent genes (86 protein-coding, 37 tRNA, and 8 rRNA), and there are 18 repeated genes within the IR region. Among these genes, 17 genes contained one or two introns. The phylogenetic analysis showed that R. davurica was relatively close to other Rosa species, such as the Rosa hybrid.

Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus

BACKGROUND

Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species.

RESULTS

In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize.

CONCLUSION

Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.

PROGRAMMED CELL DEATH8 interacts with tetrapyrrole biosynthesis enzymes and ClpC1 to maintain homeostasis of tetrapyrrole metabolites in Arabidopsis

Tetrapyrrole biosynthesis (TBS) is a dynamically and strictly regulated process. Disruptions in tetrapyrrole metabolism influence many aspects of plant physiology, including photosynthesis, programmed cell death (PCD), and retrograde signaling, thus affecting plant growth and development at multiple levels. However, the genetic and molecular basis of TBS is not fully understood. We report here PCD8, a newly identified thylakoid-localized protein encoded by an essential gene in Arabidopsis. PCD8 knockdown causes a necrotic phenotype due to excessive chloroplast damage. A burst of singlet oxygen that results from overaccumulated tetrapyrrole intermediates upon illumination is suggested to be responsible for cell death in the knockdown mutants. Genetic and biochemical analyses revealed that PCD8 interacts with ClpC1 and a number of TBS enzymes, such as HEMC, CHLD, and PORC of TBS. Taken together, our findings uncover the function of chloroplast-localized PCD8 and provide a new perspective to elucidate molecular mechanism of how TBS is finely regulated in plants.

New insight into the genetic basis of oil content based on noninvasive three-dimensional phenotyping and tissue-specific transcriptome in Brassica napus

BACKGROUND

Increasing seed oil content is the most important breeding goal in Brassica napus, and phenotyping is crucial to dissect its genetic basis in crops. To date, QTL mapping for oil content has been based on whole seeds, and the lipid distribution is far from uniform in different tissues of seeds in B. napus. In this case, the phenotype based on whole seeds was unable to sufficiently reveal the complex genetic characteristics of seed oil content.

RESULTS

Here, the three-dimensional (3D) distribution of lipid was determined for B. napus seeds by magnetic resonance imaging (MRI) and 3D quantitative analysis, and ten novel oil content-related traits were obtained by subdividing the seeds. Based on a high-density genetic linkage map, 35 QTLs were identified for 4 tissues, the outer cotyledon (OC), inner cotyledon (IC), radicle (R) and seed coat (SC), which explained up to 13.76% of the phenotypic variation. Notably, 14 tissue-specific QTLs were reported for the first time, 7 of which were novel. Moreover, haplotype analysis showed that the favorable alleles for different seed tissues exhibited cumulative effects on oil content. Furthermore, tissue-specific transcriptomes revealed that more active energy and pyruvate metabolism influenced carbon flow in the IC, OC and R than in the SC at the early and middle seed development stages, thus affecting the distribution difference in oil content. Combining tissue-specific QTL mapping and transcriptomics, 86 important candidate genes associated with lipid metabolism were identified that underlie 19 unique QTLs, including the fatty acid synthesis rate-limiting enzyme-related gene CAC2, in the QTLs for OC and IC.

CONCLUSIONS

The present study provides further insight into the genetic basis of seed oil content at the tissue-specific level.

The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis

Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).

Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species

Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.