Plastome Structure Research Articles

Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns.

Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns. This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants. Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI. The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes. Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.

Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae)

The Cleisostoma–Gastrochilus clades are among the most speciose and diverse groups of Asian orchids and are a taxonomically problematic group. Phylogenetic relationships among the genera of these clades have remained unresolved with traditional sequences from one or a few markers. We present large-scale phylogenomic data sets, incorporating complete chloroplast genome sequences from 53 species (including 41 species sequenced in this study), to compare plastome structure and to resolve the phylogenetic relationships of these clades. The plastomes of Cleisostoma–Gastrochilus clades possessed the quadripartite structure and plastome genes of typical angiosperms with sizes ranging from 142 to 149 kb and encoding a set of 118–120 genes. Unusual structural features were detected in the plastome of Uncifera acuminata, including the presence of a large 17-kb inversion (19 genes) in the Large Single-Copy region and the loss of the rpl32 gene in Cleisostoma fuerstenbergianum. The pseudogenization of ndh genes was widespread in these clades. Phylogenomic analyses, including 68 plastid protein-coding genes, showed that these clades can be subdivided into three major groupings and six subgroupings: Vandopsis undulata, the Gastrochilus clade (including the Trichoglottis and Gastrochilus subclades) and the Cleisostoma clade (including the Vandopsis, Diploprora, Cleisostoma and Schoenorchis subclades). Two genera, Vandopsis and Cleisostoma, were not monophyletic. A new genus, Cymbilabia, was proposed to avoid non-monophyly of Vandopsis. Our results demonstrate the power of plastid phylogenomics to improve the phylogenetic relationships of intricate groups and provide new insight into plastome evolution in Orchidaceae.

Complete plastome sequences of two Neottia species and comparative analysis with other Neottieae species (Orchidaceae)

The tribe Neottieae (Orchidaceae subfam. Epidendroideae) represents an excellent potential system for understanding plastome evolution in orchids. The tribe includes about 100 species with six recognized genera and includes both chlorophyllous and achlorophyllous taxa. Previously published Neottieae plastomes have revealed a complicated history of gene loss, particularly ndh gene loss, as well as plastome structural changes in achlorophyllous taxa. However, the plastome structure of most Neottieae taxa remains unknown. Here we investigate plastome structure in two newly sequenced Neottia species (N. suzukii and N. japonica) and characterize sequence divergence among Neottieae plastomes. We sequenced and analysed the complete plastomes of three individuals of two Neottia species (two individuals of N. japonica and one individual of N. suzukii) and compared them to seven additional published Neottia plastomes. The total genome lengths of the plastomes of N. japonica and N. suzukii ranged from 156,978 to 157,326 bp. The newly sequenced plastomes possessed the typical structure and gene content of angiosperm plastomes. Phylogenetic analyses based on complete plastomes and the nuclear internal transcribed spacer (ITS) showed that N. japonica and N. suzukii form a clade, but the two accessions of N. japonica were in phylogenetically incongruent positions in ITS vs plastome trees. Among all three newly sequenced Neottia plastomes, five regions (ndhH-ndhA spacer, ndhA intron, ycf3 intron, atpF intron, and trnL-ndhB spacer) showed high nucleotide divergence values (> 0.15), and are therefore considered useful molecular markers for future phylogenetic and phylogeographic studies of Neottia.

Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be differentiated with marked sequence variation and different inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae.

Exploring the plastid genome disparity of liverworts

AbstractSequencing the plastid genomes of land plants provides crucial improvements to our understanding of the plastome evolution of land plants. Although the number of available complete plastid genome sequences has rapidly increased in the recent years, only a few sequences have been yet released for the three bryophyte lineages, namely hornworts, liverworts, and mosses. Here, we explore the disparity of the plastome structure of liverworts by increasing the number of sequenced liverwort plastomes from five to 18. The expanded sampling included representatives of all major lineages of liverworts including the genus Haplomitrium. The disparity of the liverwort genomes was compared with other 2386 land plant plastomes with emphasis on genome size and GC‐content. We found evidence for structural conservatism of the plastid genomes in liverworts and a trend towards reduced plastome sequence length in liverworts and derived mosses compared to other land plants, including hornworts and basal lineages of mosses. Furthermore, Aneura and Haplomitrium were distinct from other liverworts by an increased GC content, with the one found in Haplomitrium only second to the lycophyte Selaginella. The results suggest the hypothesis that liverworts and other land plants inherited and conserved the plastome structure of their most recent algal ancestors.

The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats.

The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.

Dynamism in plastome structure observed across the phylogenetic tree of ferns

Dynamism in plastome structure observed across the phylogenetic tree of ferns

Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen.

We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

Order-level fern plastome phylogenomics: new insights from Hymenophyllales.

Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one-cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order. We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters. We discovered a suite of novel, Hymenophyllales-specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non-Osmundales leptosporangiates, depending on the data type and partition scheme. Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.

Chloroplasts: Structure and Expression of the Plastid Genome

During the last two decades much success in studying plastid genome structure and expression was achieved. The primary sequence of hundreds of plant plastid genomes has been determined, which allows us to understand basic laws of plastome structure. Novel chloroplast nuclear-encoded RNA-polymerases and sigma-factors have been discovered. Mechanisms responsible for posttranscriptional regulation of plastid genes' expression, including splicing and editing, are actively being studied. Increasingly more data on the most important role of nucleoids in chloroplast biogenesis is emerging. Much attention is presently given to studying the proteins associated with bacterial type RNA-polymerase. Determination of the primary sequence of genomes for a number of higher plants has produced new information on the exchange of genetic material between cell organelles. At present, interorganelle signaling in plant cells is a subject of active study. In the review, a wide range of issues is quite briefly discussed, including some elements of chloroplast evolution and nuclear-plastid signaling. Certain features of chloroplast genetic material organization are described. In addition, basic stages of plastid genome expression are discussed.

Passifloraplastome sequencing reveals widespread genomic rearrangements

AbstractAlthough past studies have includedPassifloraamong angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling ofPassifloraplastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15Passifloraplastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. ThePopulus trichocarpaplastome was used as a reference to estimate genomic rearrangements inPassifloraby performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames,ycf1andycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) inP. biflorato 161 494 bp inP. pittieri.Passifloraplastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. EachPassiflorasubgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows thatPassiflorahas experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.

The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae

Crambe abyssinica is an important oilseed crop that accumulates high levels of erucic acid, which is being recognized as a potential oil platform for several industrial purposes. It belongs to the family Brassicaceae, assigned within the tribe Brassiceae. Both family and tribe have been the subject of several phylogenetic studies, but the relationship between some lineages and genera remains unclear. Here, we report the complete sequencing and characterization of the C. abyssinica plastome. Plastome structure, gene order, and gene content of C. abyssinica are similar to other species of the family Brassicaceae. The only exception is the rps16 gene, which is absent in many genera within the family Brassicaceae, but seems to be functional in the tribe Brassiceae, including C. abyssinica. However, the analysis of gene divergence shows that the rps16 is the most divergent gene in C. abyssinica and within the tribe Brassiceae. In addition, species of the tribe Brassiceae also show similar SSR loci distribution, with some regions containing a high number of SSRs, which are located mainly at the single copy regions. Six hotspots of nucleotide divergence among Brassiceae species were located in the single copy regions by sliding window analysis. Brassicaceae phylogenomic analysis, based on the complete plastomes of 72 taxa, resulted in a well-supported and well-resolved tree. The genus Crambe is positioned within the Brassiceae clade together with the genera Brassica, Raphanus, Sinapis, Cakile, Orychophragmus and Sinalliaria. Moreover, we report several losses and gains of RNA editing sites that occurred in plastomes of Brassiceae species during evolution.

Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales.

Premise of the Study Toona (Meliaceae, Sapindales) is a small genus of five species of trees native from southern and eastern Asia to New Guinea and Australia. Complete plastomes were sequenced for three Toona species to provide a basis for future plastome genetic studies in threatened species of Toona. In addition, plastome structural evolution and phylogenetic relationships across Sapindales were explored with a larger data set of 29 Sapindales plastomes (including members of six out of nine families).MethodsThe plastomes were determined using the Illumina sequencing platform; the phylogenetic analyses were conducted using maximum likelihood by RAxML.ResultsThe lengths of three Toona plastomes range from 159,185 to 158,196 bp. A total of 113 unique genes were found in each plastome. Across Sapindales, plastome gene structure and content were largely conserved, with the exception of the contraction of the inverted repeat region to exclude ycf1 in some species of Rutaceae and Sapindaceae, and the movement of trnI‐GAU and trnA‐UGC to a position outside the inverted repeat region in some Rutaceae species.DiscussionThe three Toona plastomes possess the typical structure of angiosperm plastomes. Phylogenomic analysis of Sapindales recovered a mostly strongly supported phylogeny of Sapindales, including most of the backbone relationships, with some improvements compared to previous targeted‐gene analyses.

Evolution of Geosiris (Iridaceae): historical biogeography and plastid-genome evolution in a genus of non-photosynthetic tropical rainforest herbs disjunct across the Indian Ocean

Mycoheterotrophs, i.e. plants that acquire carbon from root-associated soil fungi, often have highly degraded plastomes, reflecting relaxed selective constraints on plastid genes following the loss of photosynthesis. Geosiris Baill. is the only mycoheterotrophic genus in Iridaceae and comprises two species in Madagascar and nearby islands, and a third recently discovered species in north-eastern Australia. Here, we characterise the plastomes of the Australian and one Madagascan species to compare patterns of plastome degradation in relation to autotrophic and other mycoheterotrophic taxa and investigate the evolutionary and biogeographical history of the genus in Iridaceae. Both examined species have lost approximately half their plastid-encoded genes and a small but significant reduction in purifying selection in retained non-photosynthetic genes was observed. Geosiris is confirmed as monophyletic, with initial divergence of the genus occurring c. 53 million years ago, and subsequent diversification occurring c. 30 million years ago. Africa (including Madagascar) is reconstructed as the most likely ancestral area of the genus, implying a major range-expansion event of one lineage to Australia after its divergence in the Oligocene. Our study has highlighted the dynamic evolutionary history of Geosiris, contributed to the characterisation of mycoheterotrophic plastomes, and furthered our understanding of plastome structure and function.

Sequencing of the plastome in the leafless green mycoheterotroph Cymbidium macrorhizon helps us to understand an early stage of fully mycoheterotrophic plastome structure

To date, plastome studies of mycoheterotrophic orchids have focused on nongreen mycoheterotrophic or partially mycoheterotrophic species. Cymbidium macrorhizon is a fully mycoheterotrophic orchid that lacks leaves and roots, although its inflorescence rachis is pale green. It has degraded stomata, specific fungal partners, and high concentrations of heavy stable nitrogen and carbon isotopes. Therefore, the plastome of this species is expected to represent an early stage of a fully mycoheterotrophic plastome. In this study, we sequenced the plastomes of C. macrorhizon and closely related species (C. ensifolium, C. kanran, and C. lancifolium). Plastomes of the four Cymbidium species were almost identical structurally, but differed somewhat from those of previously studied species. The genes for the photosynthetic subunits of NADH dehydrogenase, ndhF and ndhH, were absent from all four newly sequenced plastomes, whereas only ndhJ was absent from C. ensifolium. In section Pachyrhizanthe (C. lancifolium and C. macrorhizon), ndhE, ndhI, and ndhJ were pseudogenized. With the exception of ndh and ycf, 64 protein-coding genes in C. macrorhizon were apparently functional. Most of them were highly conserved and under purifying selection. Therefore, no direct evidence is available to suggest that genes related to photosynthesis have lost their functions in C. macrorhizon. This discordance between molecular and physiological features for the trophic status of C. macrorhizon might result from a lag between photosynthetic function loss and relaxed purifying selection.

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family

BackgroundAmong the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae.ResultsUsing an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae.Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses.ConclusionThe first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales.

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae).

BackgroundComparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex.MethodsGenomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed.ResultsThe plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae.DiscussionThe complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex, representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

Diversity and evolution of plastomes in Saharan mimosoids: potential use for phylogenetic and population genetic studies

Acacias (Mimosoideae) represent a major woody group in arid and subarid habitats of all tropical and subtropical regions. The genetic diversity and population dynamic of African species are still poorly investigated, in particular due to ploidy variation among and within species. Here, we aim to investigate the diversity of the plastid genome (or plastome) of Central Saharan mimosoids, in order to assess its potential utility for phylogenetic and population genetic analyses. We first used a genome skimming strategy to assemble the complete plastome plus the nuclear ribosomal DNA cluster of six species belonging to three genera (Vachellia, Senegalia, and Faidherbia). Phylogenetic relationships based on these data confirm the existence of three main evolutionary lineages in the Hoggar range (southern Algeria). An analysis of the plastome structure reveals an extension of the inverted repeat (IR) in Faidherbia albida as recently reported in two other genera of the same lineage (Inga and Acacia s.s.). Higher substitution rates are detected in this lineage, and our species sampling allows revealing genes (particularly accD, clpP, rps2, rps3, ycf1, ycf2, and ycf4) under positive selection following the IR extension. The reasons for this evolutionary transition need to be unraveled. We then develop 21 plastid microsatellites to be used on a large panel of mimosoid species. At a local scale, 18 of these loci reveal intra-specific polymorphism in at least one species. These markers may be useful to assess the genetic diversity of the plastome for comparative phylogeographies or population genetic studies.

Chloroplasts: state of research and practical applications of plastome sequencing

Main conclusionThis review presents origins, structure and expression of chloroplast genomes. It also describes their sequencing, analysis and modification, focusing on potential practical uses and biggest challenges of chloroplast genome modification.During the evolution of eukaryotes, cyanobacteria are believed to have merged with host heterotrophic cell. Afterward, most of cyanobacterial genes from cyanobacteria were transferred to cell nucleus or lost in the process of endosymbiosis. As a result of these changes, a primary plastid was established. Nowadays, plastid genome (plastome) is almost always circular, has a size of 100–200 kbp (120–160 in land plants), and harbors 100–120 highly conserved unique genes. Plastids have their own gene expression system, which is similar to one of their cyanobacterial ancestors. Two different polymerases, plastid-derived PEP and nucleus-derived NEP, participate in transcription. Translation is similar to the one observed in cyanobacteria, but it also utilizes protein translation factors and positive regulatory mRNA elements absent from bacteria. Plastoms play an important role in genetic transformation. Transgenes are introduced into them either via gene gun (in undamaged tissues) or polyethylene glycol treatment (when protoplasts are targeted). Antibiotic resistance markers are the most common tool used for selection of transformed plants. In recent years, plastome transformation emerged as a promising alternative to nuclear transformation because of (1) high yield of target protein, (2) removing the risk of outcrossing with weeds, (3) lack of silencing mechanisms, and (4) ability to engineer the entire metabolic pathways rather than single gene traits. Currently, the main directions of such research regard: developing efficient enzyme, vaccine antigen, and biopharmaceutical protein production methods in plant cells and improving crops by increasing their resistance to a wide array of biotic and abiotic stresses. Because of that, the detailed knowledge of plastome structure and mechanism of functioning started to play a major role.