Search Results (588)

Diospyros, the most species-rich woody plant genus in Ebenaceae, has attracted significant academic interest due to its ecological and economic importance. This study presented the first complete assembly and annotation of the chloroplast genome of Diospyros tsangii. The chloroplast genome measured 157,445 bp, with a typical quadripartite circular structure and 132 annotated coding genes. A comprehensive analysis of evolutionary traits and codon usage preferences across chloroplast genomes of 15 Diospyros species were conducted. The main objective was to provide a theoretical basis for understanding phylogenetic relationships and assessing genetic diversity within Diospyros. Our findings showed that genetic diversity in the IR regions of the chloroplast genomes is notably lower than that in the LSC and SSC regions. The boundary regions exhibited high conservation with minimal variation. Selected pressure analysis indicated that most coding genes are under purifying selection. Phylogenetic analysis showed that D. tangii was sister to Diospyros oleifera, and Diospyros kaki was closely related to Diospyros vaccinioides with high supporting values. The examination of codon usage patterns showed that the GC content at the first, second, and third codon positions of 52 protein-coding sequences followed the order GC1 > GC2 > GC3, with a preference for A or U bases at the third position. The effective number of codons ranged from 45.13 to 45.43, which indicated the weak codon bias. The neutral-plot, ENC-plot, and PR2-plot analysis suggested that natural selection predominantly influences the codon usage patterns in Diospyros plants. These results would be vital to understand the evolutionary dynamics of the genus Diospyros. Full article

Nitrogen assimilation is vital for apple growth, yield, and quality, with nitrate reductase (NIA), nitrite reductase (NIR), glutamine synthetase (GS), and glutamate synthase (GOGAT) serving as key regulatory enzymes. This study systematically identified these four gene families in apple (Malus domestica) through genome-wide analysis and examined their expression patterns under nitrate treatment. In total, 13 genes were identified, 2 MdNIAs, 1 MdNIR, 7 MdGSs, and 3 MdGOGATs, with gene lengths ranging from 2577 to 27736 base pairs (bp); MdGLT1A had the longest coding sequence (6627 bp). The encoded proteins contained 355–2208 amino acids, with predicted isoelectric points (pIs) between 5.55 and 6.63. Subcellular localization analysis predicted distinct compartmentalization: MdNIA1A in peroxisomes; MdGS1 in the cytosol; MdNIR1, MdGS2, and MdGLU1 in chloroplasts; and MdGLT1 in mitochondria/chloroplasts. Functional site prediction revealed multiple phosphorylation and glycosylation sites, with ATP/GTP-binding motifs present only in certain MdGOGAT proteins. Protein interaction analysis suggested close associations among these genes and possible interactions with NRT2.1/2.2. Chromosomal mapping showed their distribution across eight chromosomes, while promoter analysis identified diverse cis-acting regulatory elements (e.g., ABRE and G-box). Under nitrate treatment (0–12 h), these genes exhibited distinct expression dynamics: MdNIA1A and B were rapidly induced (0–6 h) and maintained high expression; MdNIR1 peaked at 6 h and then declined; MdGS1.1B was activated after 6 h; and MdGS2A, MdGLU1, and MdGLT1A/B peaked at 6 h before decreasing. Therefore, these results elucidate the structural and functional divergence of nitrogen assimilation genes in apple and provide a basis for understanding nitrogen utilization mechanisms and developing nitrogen-efficient breeding strategies. Full article

Grapes (Vitis spp.) are a globally significant fruit crop with a long history of cultivation and substantial cultivar diversity. Their high genetic differentiation and complex evolutionary history make them a valuable system for studying plant evolution. The chloroplast genome, known for its structural conservation and uniparental inheritance, offers a reliable molecular marker for phylogenetic reconstruction. In this study, we sequenced and assembled the complete chloroplast genomes of nine representative grape cultivars, analyzed their phylogenetic relationships, and compared structural variations. All chloroplast genomes displayed a typical quadripartite structure, with high conservation in genomic architecture, gene order and content, codon usage, and simple sequence repeats (SSRs). However, additional sequence comparisons revealed seven regions with high variation, including the genes rbcL and ndhF, and the intergenic regions rps16-trnQ, ndhC-trnV, accD-psaI, ndhF-rpl32, and trnL-ccsA. At the same time, seven natural variation sites were identified in the amino acid sequences of rbcL and ndhF. Additionally, the study’s maximum likelihood (ML) phylogenetic trees and photosynthetic index measurements suggest that developmental characteristics of grape photosynthesis may be related to the evolutionary origins of different populations. This phylogenetic classification not only elucidates the evolutionary origins of these germplasm resources but also provides a foundation for molecular-assisted breeding by identifying distinct genetic groups. Full article

[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of E. tubulosa and E. japonica—two medicinal plants belonging to the genus Euchresta—this study aims to identify their differential genes, thereby providing fundamental research for screening candidate genes as DNA barcodes for species identification and facilitating the conservation of these endangered species. [Methods]: Illumina PE150 sequencing was performed. Chloroplast genomes (plastomes) were assembled and annotated with GetOrganelle/SPAdes. Comparative analyses assessed gene content, IR/LSC/SSC structure, repeat profiles, and codon-usage bias. Using related Fabaceae as references, we conducted mVISTA alignments and sliding-window nucleotide diversity (Pi) analyses to identify candidate DNA barcodes. Phylogenies from whole-plastome sequences were inferred with Maximum Likelihood, Bayesian Inference, and Maximum Parsimony. [Results]: The plastomes measured 153,960 bp (E. japonica) and 150,146 bp (E. tubulosa), with GC contents of 36.30% and 36.20%, respectively, each exhibiting a typical quadripartite structure. IR/SC boundaries were highly conserved without evident expansion or contraction. Repeat statistics were 20/30 palindromic repeats, 57/64 tandem repeats, and 156/159 simple sequence repeats (SSRs) in E. japonica/E. tubulosa, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci—rps19, psbA, trnK, matK, and rps16 (Pi > 0.03)—were identified as candidate DNA barcodes. All trees consistently placed both species within Papilionoideae (Fabaceae) and recovered the closest relationship to Sophora macrocarpa. [Conclusions]: This study provides, for the first time, complete plastomes and candidate barcoding regions for two protected Euchresta species, supplying foundational resources for species identification, resource assessment, and conservation planning. Full article

Brassica juncea var. multiceps (Xuelihong), a variety of B. juncea (L.) Czern., holds considerable nutritional and economic value. However, its complete chloroplast genome and the evolutionary relationships within Brassicaceae remain poorly characterized. Using Illumina NovaSeq 6000 high-throughput sequencing, we assembled and annotated the full chloroplast genome sequence of B. juncea var. multiceps. The genome is 153,483 bp in length, with 36.36% GC content, and encodes 132 genes. Codon usage analysis identified leucine (Leu) as the dominant amino acid. Thirty-one codons had relative synonymous codon usage (RSCU; a metric for codon preference) values greater than one, with 93.55% of these preferred codons ending in A/U. We detected 37 dispersed repeats (14 forward, 18 palindromic, 3 reverse, and 2 complementary) and 315 simple sequence repeats (SSRs), with mononucleotide SSRs dominating (72.70%). Analysis of the Ka/Ks ratio, a measure of selection pressure (where values greater than one indicate positive selection), indicated that ycf1, ycf2, and nadhF genes may have undergone positive selection. The nucleotide diversity analysis revealed five hypervariable hotspot-genomic regions with high mutation rates, which are critical for phylogenetic studies. Phylogenetic analysis of 26 Brassicaceae species revealed that B. juncea var. multiceps is closely related to B. juncea. Notably, this is the first complete chloroplast genome of B. juncea var. multiceps, with unique hypervariable regions not reported in other B. juncea varieties. These findings clarify evolutionary relationships in Brassicaceae, provide molecular markers for the genetic breeding of B. juncea var. multiceps, and enhance our understanding of chloroplast genome adaptation in Brassica. Full article

Background/Objectives: Macadamia integrifolia is a valuable subtropical fruit tree, yet genomic studies on its cultivars are limited. This study aims to elucidate the chloroplast genome features, variations, and phylogenetic relationships of three main cultivars (‘Guilin No. 1’, ‘Nanya No. 1’, ‘Qian’ao No. 1’) to support germplasm identification and breeding. Methods: chloroplast genomes of three M. integrifolia cultivars from Guangxi, Guangdong, and Guizhou were sequenced using Illumina technology, followed by assembly, annotation, and comparative analyses of structure, repeats, and codon usage. Phylogenetic relationships were reconstructed using complete genome sequences. Results: The three chloroplast genomes displayed typical quadripartite structures, with lengths of 159,714 bp, 159,195 bp, and 159,508 bp, and GC contents of 38.12%, 38.16%, and 38.14%, respectively. Each encoded 135 genes. Codon usage was biased towards A/U-ending codons. We identified 81, 87, and 80 SSRs and 26, 21, and 20 long repeats, respectively. IR boundary regions were highly conserved. Phylogenetically, the cultivars showed close relationships with M. integrifolia, Macadamia tetraphylla, and Macadamiaternifolia, forming a sister clade to Platanus occidentalis. Conclusions: This study provides essential chloroplast genomic resources for three M. integrifolia cultivars, revealing conserved structures and specific variations. The findings offer crucial insights for the genus's genetic diversity, supporting future germplasm evaluation and phylogenetic research. Full article

Chloroplast codon usage bias (CUB) records both maternal phylogeny and selection intensity. Characterizing CUB in the synthetic cereal × Triticosecale and its Triticum and Secale parents is therefore a prerequisite for plastid-based engineering and for tracing the evolutionary consequences of recent allopolyploidy. Complete plastome sequences of five taxa—Triticum monococcum, T. turgidum, T. aestivum, Secale cereale and × Triticosecale sp.—were downloaded. Protein-coding genes were extracted to calculate overall GC, GC1–GC3, SCUO, RSCU, ENC-GC3s, neutrality, and PR2 plots. Optimal codons were defined as RSCU ≥ 1 and △RSCU ≥ 0.8. The results showed that the chloroplast genomes of these five species are low in GC content for the third base of codons, suggesting an end preference for A or U bases. The SCUO values ranged from 0.22 to 0.23, suggesting no significant codon usage bias. GC content was relatively low (38.78–39.16%), with the order GC1 > GC2 > GC3. RSCU analysis indicated that codons ending with A/T are more commonly used. Neutral mapping, ENC-GC3s, and the PR2 plot all showed that the preference of codon usage for the majority of functional genes was influenced by a combination of mutation and natural selection pressure, and the influence of natural selection was predominant. RSCU clustering recovers the expected maternal tree (Triticum clade + triticale). All optimal codons terminate with A or U, yielding identical plastid translation tables for the five species. Despite its recent hybrid origin, triticale plastid CUB is indistinguishable from its wheat maternal ancestor and is governed mainly by selection. The compiled optimal codon set provides an immediate reference for chloroplast transformation and for dissecting selection relaxation in newly synthesized triticale combinations. Full article

RNA editing is a crucial mechanism regulating gene expression in plant organellar genomes, which optimizes protein structures through base substitution and plays a vital role in plant growth, development, and stress adaptation. This study revises the conventional understanding restricting MORF proteins to seed plants by reporting their first identification in ferns, an early vascular plant lineage. We sequenced chloroplast genomes of O. japonica and P. vachellii, revealing one MORF9 homolog in O. japonica and three homologs (MORF1/8/9) in P. vachellii through comparative transcriptomics and structural validation. All identified MORF proteins harbor conserved MORF-box domains, suggesting structural and potentially functional conservation with angiosperms. Crucially, MORF members differentially regulate organellar RNA editing: chloroplast editing frequencies are predicted to show dose-dependent enhancement (0.7–1.0 in conserved sites), potentially influenced by MORF presence or copy number. In O. japonica, chloroplast editing exhibits tissue-specific patterns (conserved sites 0.7–1.0; tissue-specific sites lower efficiency at 0.1–0.2), while this study’s mitochondrial editing results show a balanced frequency distribution (0–1 range). Amino acid substitution analysis demonstrates MORF-mediated hydrophobic optimization (Ser→Leu > 30%, Pro→Leu > 18%), likely underpinning fern adaptability. This work provides crucial initial evidence for a conserved MORF-mediated RNA editing module shared between these early vascular plants (ferns) and angiosperms, offering fundamental insights into the evolutionary trajectory of plant organellar gene regulation. Full article

Dendrobium is an orchid genus with high economic and ecological importance, but its taxonomy based on morphology remains controversial. Dendrobium linawianum, a critically endangered species with both ornamental and medicinal value, represents a key taxon within this genus. However, its phylogenetic relationship has long been unplaced due to similar morphological traits. Despite its conservation and taxonomic importance, its complete chloroplast genome has not been previously characterized. Here, we newly sequenced and assembled the complete chloroplast genome of D. linawianum. The 150,497 bp genome exhibits a typical quadripartite structure, encoding 119 genes. A total of 161 simple sequence repeats (SSRs) were identified, predominantly mononucleotide and dinucleotide motifs. Condon usage analysis revealed leucine as the most abundant amino acid. Phylogenetic analysis based on complete chloroplast genome sequences strongly supported the close relationship of D. linawianum with D. hercoglossum, D. thyrsiflorum, and D. moniliforme, resolving its taxonomic position within the genus. The complete chloroplast genomes successfully resolved the phylogenetic relationships among 35 Dendrobium species, demonstrating their efficacy as powerful molecular markers for resolving taxonomic ambiguities within this morphologically complex genus. Our findings provide a genomic foundation for precise species identification and molecular breeding of D. linawianum, and enhance understanding of phylogenetic relationships in this taxonomically challenging group. Full article

Rice blast, caused by Magnaporthe oryzae (M. oryzae), severely threatens global rice production with substantial yield losses, endangering food security and driving demand for resistant varieties. Fuhui2165 (FH2165), an elite restorer line with stable blast resistance, superior agronomic traits, and high grain quality, is valuable for hybrid breeding, but its resistance mechanisms remain unclear. In this study, we investigated the rice blast resistance and underlying mechanisms in FH2165 and its parental lines (Huahangsimiao/HHSM, Minghui86/MH86, and Shuhui527/SH527) using transcriptome sequencing analysis. Phenotypic analysis revealed that FH2165 and HHSM exhibited stronger resistance compared to MH86 and SH527. Differential expression analysis identified 3886, 2513, 3390, and 4678 differentially expressed genes (DEGs) in FH2165, HHSM, MH86, and SH527, respectively. Gene Ontology (GO) enrichment analysis highlighted DEGs associated with chloroplasts, plastids, thylakoids, and related cellular components. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified significant enrichment in pathways such as carbon metabolism, amino acid biosynthesis, and photosynthesis. This suggested that defense strategies could involve energy reprogramming and the synthesis of secondary metabolites. Additionally, the DEGs co-expressed specifically in FH2165 and HHSM were enriched in functions related to RNA processing, GTP binding, and L-ascorbic acid binding, with purine metabolism playing a role in the regulation of energy and signaling. These findings elucidated the critical metabolic and signaling networks that underlie the blast resistance of FH2165 and offered potential targets for breeding high-yield, disease-resistant hybrid rice varieties. Full article

Background/Objectives: Species within section Chrysantha represent the only camellias known to produce golden-yellow petals. The primary objectives of this study were to characterize the chloroplast genome structure of Camellia tianeensis and to elucidate its phylogenetic position with sect. Chrysantha. Methods: The complete chloroplast genome of C. tianeensis was sequenced, assembled, and annotated. Phylogenetic inference was conducted using maximum likelihood and Bayesian methods based on complete chloroplast genomic sequences. Results: The chloroplast genome of C. tianeensis is 156,865 bp in length and exhibits a typical quadripartite structure consisting of a large single-copy (LSC) region (86,579 bp), a small single-copy (SSC) region (18,236 bp), and two inverted repeat (IR) regions (26,025 bp each). The genome encodes 164 genes, including 111 protein-coding genes, 45 tRNAs, and 8 rRNA genes. The overall GC content was 37.32%, with regional values of 35.33% (LSC), 30.59% (SSC), and 42.99% (IRs). Sixty-nine simple sequence repeats (SSRs) were identified, predominantly mononucleotide repeats, Thirty-eight dispersed repeats were categorized into three types (forward, reverse, and palindromic), with no complement repeats detected. Phylogenetic analysis strongly supported that C. tianeensis is a member within sect. Chrysantha. Conclusions: C. tianeensis is phylogenetically closely related to C. huana, forming a well-supported clade. This study enhances the molecular research available for sect. Chrysantha and provides a genomic foundation for future phylogenetic and taxonomic studies in this group. Full article

Hygrophila polysperma is a type of amphibious plant that originates from Acanthaceae. Here, we report its first complete chloroplast (cp) genome. The complete cp genome is 146,675 bp in length with 38.3% of GC content. There are 130 genes including 86 protein coding genes, 36 tRNA genes, and 8 rRNA genes in this genome. Simple short sequence (SSR) analysis found 30 SSRs, 24 of which are located in a large single-copy region. Nucleotide diversity identified six most divergent sequences (trns-GCU, psaA-pafI, psaI-pafII, ycf2, rpl32, and ycf1) among 3 close-related species, H. polysperma, H. ringens, and Asteracantha longifolia. A phylogenetic tree among H. polysperma and another 30 related species was constructed based on the common coding sequence of the cp genome and showed that H. polysperma is most closely related to H. ringens (both belong to subtribe Hygrophilinae) and, together, they form a clade that is sister to A. longifolia. This study provides a basis for systemic and evolution studies as well as the development of molecular markers for species identification and genetic breeding. Full article

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development. Full article

Camellia sinensis cv. Xinyang10 is a nationally recognized elite tea cultivar selected from the Xinyang drought-resistant population, valued for its notable cold tolerance and broad adaptability. In this study, we present the first complete assembly and annotation of its mitogenome. The mitogenome features a multipartite structure, consisting of a circular chromosome (798,917 bp) and a linear chromosome (46,159 bp), harboring a total of 74 genes. We identified extensive repetitive sequences (244 simple sequence repeats and 998 long sequence repeats), 211 RNA editing sites, and 16,614 bp of chloroplast-derived DNA, indicating a highly dynamic genome. Positive selection was detected in nad1 and ccmFC. Phylogenetic analysis based on mitochondrial SNP markers placed C. sinensis Xinyang10 closest to C. sinensis var. pubilimba. Notably, a phylogeny reconstructed based on mitogenomic collinearity displayed a distinct geographical pattern, supporting the hypothesized westward-to-eastward migration route of tea plants from southwestern China. These findings provide valuable genomic resources and demonstrate the utility of the mitogenome in understanding the evolutionary history of tea plants. Full article

The plant Actinostemma tenerum is endemic to East Asia and has been used as a traditional medicinal herb for over 1400 years. Investigating the chloroplast genome characteristics and codon usage bias (CUB) is essential for advancing research on molecular markers and genetic diversity in A. tenerum. In this study, we sequenced the complete chloroplast genome of A. tenerum, revealing a length of 160,579 bp, with a GC content of 36.5%. The genome comprised 132 coding genes, including 87 protein-coding genes (CDSs), 8 rRNA genes, and 37 tRNA genes. Analysis of the 51 selected CDSs showed average GC1, GC2, and GC3 values of 46.95%, 39.52%, and 28.11%, respectively. The effective number of codons (ENC) ranged from 35.34% to 56.23%, with an average of 45.57%, indicating a weak CUB. Nucleotide composition analysis revealed unequal distribution of A, T, C, and G, with codon preference biased towards A or U. Neutrality plots, ENC-plots, and PR2-bias plots indicated that natural selection predominantly influences on CUB. A total of 18 optimal codons were identified. This study contributes genetic insights into A. tenerum and enhances our understanding of codon usage patterns in plant chloroplast genomes. Full article