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opencc-zeroSep 2021View details →

Rhizophora complete chloroplast genome sequences

Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of Rhizophora species. Throughout the Indian Ocean, R. stylosa and R. mucronata appear as a young phylogenetic group with expansion of R. mucronata towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 R. mucronata provenances across a >4,200 km coastal stretch in the WIO using R. stylosa as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the R. stylosa chloroplast genome. A total of 58 mutations in R. mucronata encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other R. mucronata haplogroups as it was from R. stylosa. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO Rhizophora mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of R. mucronata lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.

opencc-zeroMar 2022View details →

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria

Members of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the Arabidopsis chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target rpoA site when expressed in chloroplasts and in the bacterium E. coli. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.

opencc-by-4.0Dec 2021View details →

Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae

This is all the alignments which used to constructed a phylogenetic tree in our study about Onagraceae. The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, which comprises 22 genera widely distributed from boreal to tropical areas. In the present study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved plastome sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete plastomes of Onagraceae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that chloroplast genomes are basically conserved in gene arrangement across the family. Whereas, a large segment of inversion was detected in the LSC region of all samples in the Oenothera subsect. Oenothera. An inverted repeat (IR) contraction was found in Circaea and Ludwigia samples. We also compared chloroplast genomes across the Onagraceae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference (BI) methods. The generic relationship of Onagraceae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family. Oenothera phylogeny was better resolved than other densely sampled genera. Biparental transmission may be the main cause of higher variation in the genus Oenothera.

opencc-zeroMar 2023View details →

Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis

The Himalaya-Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological Niche Models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.

opencc-by-4.0Mar 2023View details →

Datasets supporting for "Further insight into the involvement of PII1 in starch granule initiation in Arabidopsis leaf chloroplasts."

The folder contains data to support the paper entitled " Further insight into the involvement of PII1 in starch granule initiation in Arabidopsis leaf chloroplasts." The folder named "MEB pictures" contains all pictures that were used to determine starch granule size (only granules with visible major axis were measured. The folder named "confocal microscopy" contains the files used to determine starch granule number per plastid. it contains one folder for plants in Ws genetic background and another folder for plants in Col-0 genetic background.

opennotspecifiedDec 2002View details →

FIG. 2 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 2. Strict consensus tree of the 30,000 most parsimonious trees based on the combined trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 1 (not weighted) including 58 taxa; Length = 524, CI = 0.479, RI = 0.601, RC = 0.288. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.

opennotspecifiedDec 2002View details →

FIG. 1 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 1. Strict consensus tree of the 30,000 most parsimonious trees based on the 5S spacer sequence data recoverd during heuristic Search 3 for 56 taxa; Length = 231, CI = 0.519, RI = 0.743, RC = 0.386. Values above the internodes give the jackknife values (where absent, the jackknife values are less than 50%). Members of the Lampranthus group are underlined.

opennotspecifiedDec 2002View details →

FIG. 3 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 3. Strict consensus tree of the 167 most parsimonious trees based on the combined and successively weighted trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 4 including 51 taxa; CI = 0.599, RI = 0.841, RC = 0.504. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.

opencc-by-4.0Mar 2023View details →

A PETase enzyme synthesised in the chloroplast of the microalga Chlamydomonas reinhardtii is active against PET and polystyrene

The list contains: 1) raw data for chromatographies: HiprepSPHP and SEC 2) raw data for UV-vis Spectrum 3) raw data for all MS/MS spectra manuscript + supplementary 4) raw data for AFM  5) report data from HPLC

opencc-zeroMay 2023View details →

Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia

Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among the species, and we inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes or organelle localized (CECs) were significantly enriched in the introgression regions, indicating that the CEC genes of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast receptor species due to cytonuclear interactions during introgression. Notably, the intrinsic factor of cytonuclear compatibility may have a higher degree of evolutionary distance for the introgressed CEC genes between A. amurensis and A. parviflora. Introgression from A. parviflora promotes the differentiation of A. amurensis and A. japonica. Furthermore, we found that one of the overrepresented gene ontology terms in these introgressed genes was terpene synthase activity (GO: 0010333) in which more than one-third of the genes were CEC genes, showing that A. amurensis had similar release patterns for terpenes in flowers of A. parviflora when compared with A. japonica. Altogether, this study helps to clarify the mechanisms of cytonuclear coevolution, species differentiation and functional differences in face of chloroplast capture and highlights a critical role of chloroplast capture in adaptation.

Fig. 3 in The toc132toc120 heterozygote mutant of Arabidopsis thaliana accumulates decreased levels of the major chloroplast lipids

Fig. 3. Lipid molecular species in non- and cold-acclimated wildtype and toc132toc120± mutant plants as revealed by ESI-MS/MS. Values are means ± S.D. of 5 biological replicates. Asterisks above the error bars indicate significant difference (P <0.05) when compared to non-acclimated wildtype (Col-0) as determined by student's t-test.

Fig. 2 in The toc132toc120 heterozygote mutant of Arabidopsis thaliana accumulates decreased levels of the major chloroplast lipids

Fig. 2. Expression of nuclear genes that encode plastid (A) and extraplastid (B) enzymes in the wildtype and toc132toc120± mutant plants. The mRNA levels were analyzed by real-time PCR and normalized to the levels of Actin8. The expression levels in the wildtype were set to 1, and values are means ± S.E. of 4 biological replicates. Asterisks above the error bars indicate significant difference (P <0.05) when compared to non-acclimated wildtype (Col-0) as determined by student's t-test.

Fig. 1 in The toc132toc120 heterozygote mutant of Arabidopsis thaliana accumulates decreased levels of the major chloroplast lipids

Fig. 1. Total amount of lipid in each head group class in non- and cold-acclimated wildtype and toc132toc120± mutant plants. Lipid samples were analyzed on a triple quadrupole MS/MS equipped for ESI. Values are means ±S.D. of 5 biological replicates. Asterisks above the error bars indicate significant difference (P <0.05) when compared to non-acclimated wildtype (Col-0) as determined by student's t-test. CA is cold-acclimated plants.

Fig. 4 in The toc132toc120 heterozygote mutant of Arabidopsis thaliana accumulates decreased levels of the major chloroplast lipids

Fig. 4. Changes in lysophospholipids molecular species in non- and cold-acclimated wildtype and toc132toc120± mutant plants as revealed by ESI-MS/MS. Values are means ± S.D. of 5 biological replicates.