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Genes May 2024With more than 200 species of native , China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships... (Comparative Study)
Comparative Study
With more than 200 species of native , China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese species (including varieties) from three of the eight sections reported in China, i.e., the sections , , and . Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: , , , , , , intron, , and . Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these species. All sampled species formed a monophyletic group; however, sections and were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within .
Topics: Phylogeny; Genome, Chloroplast; China; Rubus; Chloroplasts
PubMed: 38927652
DOI: 10.3390/genes15060716 -
BMC Plant Biology Jun 2024Delphinium L. represents a taxonomically intricate genus of significant phylogenetic and economic importance in Ranunculaceae. Despite the existence of few chloroplast... (Comparative Study)
Comparative Study
Complete chloroplast genomes of eight Delphinium taxa (Ranunculaceae) endemic to Xinjiang, China: insights into genome structure, comparative analysis, and phylogenetic relationships.
BACKGROUND
Delphinium L. represents a taxonomically intricate genus of significant phylogenetic and economic importance in Ranunculaceae. Despite the existence of few chloroplast genome datasets, a comprehensive understanding of genome structures and selective pressures within the genus remains unknown. Furthermore, several taxa in this genus are exclusively found in Xinjiang, China, a region renowned for its distribution and diversity of Chinese and Central Asian Delphinium species. Therefore, investigating the features of chloroplast genomes in this area will provide valuable insights into the evolutionary processes and phylogenetic relationships of the genus.
RESULTS
In this study, the eight newly completed chloroplast genomes are examined, ranging in length from 153,979 bp to 154,284 bp. Alongside these, analysing six previously reported taxa re-annotated in Delphinium, 111 unique genes are identified across all samples. Genome structure, distributions of simple sequence repeats and short dispersed repeats, as well as gene content are similar among these Delphinium taxa. Nine hypervariable intergenic spacers and protein coding regions, including ndhF-trnL, rpl16-intron, rpl33, rps15, rps18, trnK-trnQ, trnP-psaJ, trnT-psbD and ycf1, are identified among 13 perennial Delphinium. Selective pressure and codon usage bias of all the plastid genes are performed within 14 Delphinium taxa. Phylogenetic analysis based on 14 Delphinium plastomes, alongside two Aconitum (Ranunculaceae) species serving as outgroup taxa, reveals the monophyletic nature of Delphinium. Our findings further discern Delphinium into two distinct clades: perennial species (clade I) and annual species (clade II). In addition, compared with the nrDNA ITS topology, cytological data and morphological characters, D. mollifolium and D. maackianum showed potential involvement in hybridization or polyploidization processes. Excluding these two species, the perennial Delphinium (clade I) exhibits a stronger consistency with the morphology-based system that utilized seed morphology.
CONCLUSION
This study represents the first comprehensive analysis of plastomic variations among Delphinium taxa, based on the examination of 14 complete plastomes. The chloroplast genome structure of Delphinium is similar to other angiosperms and possesses the typical quadripartite structure with the conserved genome arrangement and gene features. In addition, the variation of non-coding regions is larger than coding regions of the chloroplast genome. Through DNA sequence divergence across Delphinium plastomes and subsequent phylogenomic analyses ndhF-trnL and ycf1 are identified as promising molecular markers. These highly variable loci held significant potential for future phylogenetic and phylogeographic studies on Delphinium. Our phylogenomic analyses based on the whole plastomes, concatenation of 132 unique intergenic spacer regions, concatenation of 77 unique protein-coding genes and nrDNA ITS, all support the monophyly of Delphinium and perennial taxa clusters together into one clade within this genus. These findings provide crucial data for systematic, phylogenomic and evolutionary research in the genus for future studies.
Topics: Genome, Chloroplast; Phylogeny; Delphinium; China; Ranunculaceae
PubMed: 38926811
DOI: 10.1186/s12870-024-05279-y -
Environmental Microbiology Reports Jun 2024The photosynthetic amoeba, Paulinella provides a recent (ca. 120 Mya) example of primary plastid endosymbiosis. Given the extensive data demonstrating host...
The photosynthetic amoeba, Paulinella provides a recent (ca. 120 Mya) example of primary plastid endosymbiosis. Given the extensive data demonstrating host lineage-driven endosymbiont integration, we analysed nuclear genome and transcriptome data to investigate mechanisms that may have evolved in Paulinella micropora KR01 (hereinafter, KR01) to maintain photosynthetic function in the novel organelle, the chromatophore. The chromatophore is of α-cyanobacterial provenance and has undergone massive gene loss due to Muller's ratchet, but still retains genes that encode the ancestral α-carboxysome and the shell carbonic anhydrase, two critical components of the biophysical CO concentrating mechanism (CCM) in cyanobacteria. We identified KR01 nuclear genes potentially involved in the CCM that arose via duplication and divergence and are upregulated in response to high light and downregulated under elevated CO. We speculate that these genes may comprise a novel CO delivery system (i.e., a biochemical CCM) to promote the turnover of the RuBisCO carboxylation reaction and counteract photorespiration. We posit that KR01 has an inefficient photorespiratory system that cannot fully recycle the C product of RuBisCO oxygenation back to the Calvin-Benson cycle. Nonetheless, both these systems appear to be sufficient to allow Paulinella to persist in environments dominated by faster-growing phototrophs.
Topics: Carbon Dioxide; Photosynthesis; Chromatophores; Symbiosis; Amoeba; Cyanobacteria; Phylogeny
PubMed: 38923306
DOI: 10.1111/1758-2229.13304 -
The New Phytologist Jun 2024The GOLDEN2-LIKE (GLK) transcription factors act as a central regulatory node involved in both developmental processes and environmental responses. Marchantia...
The GOLDEN2-LIKE (GLK) transcription factors act as a central regulatory node involved in both developmental processes and environmental responses. Marchantia polymorpha, a basal terrestrial plant with strategic evolutionary position, contains a single GLK representative that possesses an additional domain compared to spermatophytes. We analyzed the role of MpGLK in chloroplast biogenesis and development by altering its levels, preforming transcriptomic profiling and conducting chromatin immunoprecipitation. Decreased MpGLK levels impair chloroplast differentiation and disrupt the expression of photosynthesis-associated nuclear genes, while overexpressing MpGLK leads to ectopic chloroplast biogenesis. This demonstrates the MpGLK functions as a bona fide GLK protein, likely representing an ancestral GLK architecture. Altering MpGLK levels directly regulates the expression of genes involved in Chl synthesis and degradation, similar to processes observed in eudicots, and causes various developmental defects in Marchantia, including the formation of dorsal structures such as air pores and gemma cups. MpGLK, also directly activates MpMAX2 gene expression, regulating the timing of gemma cup development. Our study shows that MpGLK functions as a master regulator, potentially coupling chloroplast development with vegetative reproduction. This illustrates the complex regulatory networks governing chloroplast function and plant development communication and highlight the evolutionary conservation of GLK-mediated regulatory processes across plant species.
PubMed: 38922903
DOI: 10.1111/nph.19916 -
Plant Cell Reports Jun 2024We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids...
We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids mitochondrial genomes. As one of the representative species in the Lauraceae family of Magnoliids, Cinnamomum camphora holds significant economic and ecological value. In this study, the mitochondrial genome (mitogenome) of C. camphora was complete assembled and annotated using PacBio HiFi sequencing. The C. camphora mitogenome is characterized by a branch structure, spans 900,894 bp, and contains 43 protein-coding genes (PCGs), 24 tRNAs, and 3 rRNAs. Most of these PCGs are under purifying selection, with only two (ccmFc and rps7) exhibiting signs of positive selection. The C. camphora mitogenome contains numerous repetitive sequences and intracellular gene transfers, with a total of 36 mitochondrial plastid DNAs, amounting to a combined length of 23,816 bp. Comparative analysis revealed that the non-coding regions of Magnoliids mitogenomes have undergone frequent rearrangements during evolution, but the coding sequences remain highly conserved (more than 98% similarity for protein-coding sequences). Furthermore, a maximum-likelihood phylogenetic tree was reconstructed based on 25 PCGs from 23 plant mitogenomes. The analysis supports the closest relationship between C. camphora and C. chekiangense, consistent with the APG IV classification system. This study elucidates the unique evolutionary features of the C. camphora mitogenome, which will provide valuable insights into the study of genetics and evolution of the family Lauraceae.
Topics: Genome, Mitochondrial; Cinnamomum camphora; Phylogeny; Evolution, Molecular; RNA, Transfer; Genome, Plant; RNA, Ribosomal
PubMed: 38922445
DOI: 10.1007/s00299-024-03256-1 -
Marine Drugs May 2024The formation of phytoene by condensing two geranylgeranyl diphosphate molecules catalyzed by phytoene synthase (PSY) is the first committed and rate-limiting step in...
The formation of phytoene by condensing two geranylgeranyl diphosphate molecules catalyzed by phytoene synthase (PSY) is the first committed and rate-limiting step in carotenoid biosynthesis, which has been extensively investigated in bacteria, land plants and microalgae. However, this step in macroalgae remains unknown. In the present study, a gene encoding putative phytoene synthase was cloned from the economic red alga -a species that has long been used in food and pharmaceuticals. The conservative motifs/domains and the tertiary structure predicted using bioinformatic tools suggested that the cloned should encode a phytoene synthase; this was empirically confirmed by pigment complementation in . This phytoene synthase was encoded by a single copy gene, whose expression was presumably regulated by many factors. The phylogenetic relationship of PSYs from different organisms suggested that red algae are probably the progeny of primary endosymbiosis and plastid donors of secondary endosymbiosis.
Topics: Rhodophyta; Phylogeny; Geranylgeranyl-Diphosphate Geranylgeranyltransferase; Carotenoids; Escherichia coli; Cloning, Molecular; Edible Seaweeds; Porphyra
PubMed: 38921568
DOI: 10.3390/md22060257 -
Current Biology : CB Jun 2024The root endophytic fungus Serendipita indica establishes beneficial symbioses with a broad spectrum of plants and enhances host resilience against biotic and abiotic...
The root endophytic fungus Serendipita indica establishes beneficial symbioses with a broad spectrum of plants and enhances host resilience against biotic and abiotic stresses. However, little is known about the mechanisms underlying S. indica-mediated plant protection. Here, we report S. indica effector (SIE) 141 and its host target CDSP32, a conserved thioredoxin-like protein, and underlying mechanisms for enhancing pathogen resistance and abiotic salt tolerance in Arabidopsis thaliana. SIE141 binding interfered with canonical targeting of CDSP32 to chloroplasts, leading to its re-location into the plant nucleus. This nuclear translocation is essential for both their interaction and resistance function. Furthermore, SIE141 enhanced oxidoreductase activity of CDSP32, leading to CDSP32-mediated monomerization and activation of NON-EXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), a key regulator of systemic resistance. Our findings provide functional insights on how S. indica transfers well-known beneficial effects to host plants and indicate CDSP32 as a genetic resource to improve plant resilience to abiotic and biotic stresses.
PubMed: 38917798
DOI: 10.1016/j.cub.2024.05.064 -
The ISME Journal Jun 2024As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally...
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.
PubMed: 38916437
DOI: 10.1093/ismejo/wrae117 -
Frontiers in Plant Science 2024The genus L. is a taxonomically complicated taxa within Apiaceae, as its high variability in morphology. Although taxonomists have performed several taxonomic revisions...
INTRODUCTION
The genus L. is a taxonomically complicated taxa within Apiaceae, as its high variability in morphology. Although taxonomists have performed several taxonomic revisions for this genus, the interspecific relationships and species boundaries have not been satisfactorily resolved, especially for those endemic to China. This study mainly focused on . var. , . var. , and var. and also described two new members of the genus.
METHODS
We newly sequenced sixteen plastomes from nine species. Combined with eleven plastomes previously reported by us and one plastome downloaded, we performed a comprehensively plastid phylogenomics analysis of 21 taxa.
RESULTS AND DISCUSSION
The comparative results showed that 21 plastomes in their structure and features were highly conserved and further justified that two new species were indeed members of Nevertheless, eleven mutation hotspot regions were still identified. Phylogenetic analyses based on plastome data and the ITS sequences strongly supported that these three varieties were clearly distant from three type varieties. The results implied that these three varieties should be considered as three independent species, which were further justified by their multiple morphological characters. Therefore, revising these three varieties into three independent species was reasonable and convincing. Moreover, we also identified and described two new species ( and ) from Sichuan and Shanxi, China, respectively. Based on their distinct morphological characteristics and molecular phylogenetic analysis, two new species were included in . In summary, our study impelled the revisions of members and improved the taxonomic system of the genus.
PubMed: 38916035
DOI: 10.3389/fpls.2024.1351023 -
BMC Biology Jun 2024Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in...
BACKGROUND
Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.
RESULTS
We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.
CONCLUSIONS
Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.
Topics: Phylogeny; Gene Transfer, Horizontal; Genome, Mitochondrial; Gnetum; DNA, Plant; Evolution, Molecular; Magnoliopsida
PubMed: 38915079
DOI: 10.1186/s12915-024-01924-y