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Wellcome Open Research 2023We present a genome assembly from cultured (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in...
We present a genome assembly from cultured (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in span. Most of the assembly is scaffolded into 44 chromosomal pseudomolecules (99.67%). The mitochondrial and plastid genomes have also been assembled, and the length of the mitochondrial scaffold is 24.3 kilobases and of the plastid genome has been assembled and is 80.2 kilobases in length.
PubMed: 38808318
DOI: 10.12688/wellcomeopenres.20345.1 -
Plant Diversity Mar 2024Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In...
Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in , which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and -statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in , and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.
PubMed: 38807911
DOI: 10.1016/j.pld.2023.10.004 -
Frontiers in Plant Science 2024is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in...
is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in evolutionary analysis and regulating respiratory-related macromolecule synthesis. In this study, the mitogenome was sequenced employing a combination of Illumina short reads and Nanopore long reads, with subsequent assembly using a hybrid strategy. We found that the predominant configuration of the mitogenome comprises two circular chromosomes. The primary structure of the mitogenome encompasses two mitochondrial chromosomes corresponding to the two major configurations, Mac1-1 and Mac1-2. The mitogenome encoded an angiosperm-typical set of 24 core genes, nine variable genes, three rRNA genes, and 15 tRNA genes. A phylogenetic analysis using the 16 shared protein-coding genes (PCG) yielded a tree consistent with the phylogeny of Lamiales species and two outgroup taxa. Mapping RNA-seq data to the coding sequences (CDS) of the PCGs revealed 507 C-to-U RNA editing sites across 31 PCGs of the mitogenome. Furthermore, one start codon (nad4L) and two stop codons (rpl10 and atp6) were identified as products of RNA editing events in the mitogenome.
PubMed: 38807783
DOI: 10.3389/fpls.2024.1326387 -
Plant Biotechnology Journal May 2024
PubMed: 38803087
DOI: 10.1111/pbi.14369 -
BMC Genomics May 2024MeFtsZ2-1 is a key gene for plant plastid division, but the mechanism by which MeFtsZ2-1 affects pigment accumulation in cassava (Manihot esculenta Crantz) through...
MeFtsZ2-1 is a key gene for plant plastid division, but the mechanism by which MeFtsZ2-1 affects pigment accumulation in cassava (Manihot esculenta Crantz) through plastids remains unclear. We found that MeFtsZ2-1 overexpression in cassava (OE) exhibited darker colors of leaves, with increased levels of anthocyanins and carotenoids. Further observation via Transmission Electron Microscopy (TEM) revealed no apparent defects in chloroplast structure but an increase in the number of plastoglobule in OE leaves. RNA-seq results showed 1582 differentially expressed genes (DEGs) in leaves of OE. KEGG pathway analysis indicated that these DEGs were enriched in pathways related to flavonoid, anthocyanin, and carotenoid biosynthesis. This study reveals the role of MeFtsZ2-1 in cassava pigment accumulation from a physiological and transcriptomic perspective, providing a theoretical basis for improving cassava quality.
Topics: Manihot; Plant Leaves; Plant Proteins; Gene Expression Regulation, Plant; Gene Expression Profiling; Transcriptome; Anthocyanins; Carotenoids; Chloroplasts; Plastids
PubMed: 38802758
DOI: 10.1186/s12864-024-10165-w -
Nature Plants Jun 2024The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA...
The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.
Topics: Nicotiana; Gene Dosage; Genome, Plastid; Inverted Repeat Sequences; Plastids; Genome Size; DNA Copy Number Variations; Genome, Plant
PubMed: 38802561
DOI: 10.1038/s41477-024-01709-9 -
Frontiers in Plant Science 2024L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes....
L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes. In this study, 23 samples of 18 species were collected from the Qinghai-Tibetan Plateau and five scattered alpine areas, and the plastid genomes (plastomes) of these species were sequenced, annotated, and compared between high-altitude and widely distributed groups. The plastomes of were found to be highly conserved in terms of gene size, content, and order but highly variable in several lineage-specific features, such as codon usage bias, IR boundary shifting, and distinct repeat sequence structures binding to SSRs. Codon usage in the genes of photosystem II exhibited an obvious preference, reflecting significant environmental adaptation pressures. In this study, three repeat regions compounded with trinucleotide and mononucleotide repeats were found for the first time in , , and . High-variability regions such as , , , and were screened, laying the foundation for the precise identification of these species. The phylogenetic analysis revealed the occurrence of cyto-nuclear discordance, likely originating from the frequent interspecific hybridization events observed within species during rapid radiation. Dioecious and hermaphrodite species can be broadly categorized into two subclades, probably they have different environmental adaptation strategies in response to climate change. In addition, the phylogenetic tree supported the monophyly of and , which compose Sect. In conclusion, plastome data enrich the genetic information available for the genus and may provide insight into species migration events during climate change.
PubMed: 38799090
DOI: 10.3389/fpls.2024.1404447 -
Plant Diversity May 2024(Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an...
(Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of . Here we conducted phylogenomic analysis by sampling populations of and its sympatric species and reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of . Both plastid and nuclear data indicate that is more closely related to , which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing was a hybrid descendant between and , with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between and in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of . By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
PubMed: 38798728
DOI: 10.1016/j.pld.2023.06.001 -
BioRxiv : the Preprint Server For... May 2024In response to environmental stress, chloroplasts generate reactive oxygen species, including singlet oxygen (O), which regulates nuclear gene expression (retrograde...
In response to environmental stress, chloroplasts generate reactive oxygen species, including singlet oxygen (O), which regulates nuclear gene expression (retrograde signaling), chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. The () mutant conditionally accumulates O and involves Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, in propagating these signals. To gain insights into O signaling pathways, we compared transcriptomes of and mutants. The accumulation of O in plants broadly repressed genes involved in chloroplast function and photosynthesis, while O induced genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA), and Salicylic acid (SA). Elevated JA and SA levels were observed in stressed plants, but were not responsible for PCD. reversed the majority of O-induced gene expression in and reduced the JA content, but maintained elevated levels of SA even in the absence of O stress. Reducing SA levels in restored O signaling and light sensitivity. Together, this work demonstrates that SA plays a protective role during photo-oxidative stress and that PUB4 mediates O signaling by modulating its levels.
PubMed: 38798329
DOI: 10.1101/2024.05.13.593788 -
Plants (Basel, Switzerland) May 2024The family Chenopodiaceae Vent. (Amaranthaceae .) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite...
The family Chenopodiaceae Vent. (Amaranthaceae .) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Thunb. species within the tribe Salsoleae ., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae . species. The size of the plastid genome varied among four species, ranging from 150,777 bp () to 151,307 bp (). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (, , , , , , , and ) were identified in ten Salsoleae . plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within species. These data represent a valuable resource for future phylogenetic studies within the genus.
PubMed: 38794403
DOI: 10.3390/plants13101332