The plastomes of Lepismium cruciforme (Vell.) Miq and Schlumbergera truncata (Haw.) Moran reveal tribe-specific rearrangements and the first loss of the trnT-GGU gene in Cactaceae.

BACKGROUND: Recent studies have revealed atypical features in the plastomes of the family Cactaceae, the largest lineage of succulent species adapted to arid and semi-arid regions. Most plastomes sequenced to date are from short-globose and cylindrical cacti, while little is known about plastomes of epiphytic cacti. Published cactus plastomes reveal reduction and complete loss of IRs, loss of genes, pseudogenization, and even degeneration of tRNA structures. Aiming to contribute with new insights into the plastid evolution of Cactaceae, particularly within the tribe Rhipsalideae, we de novo assembled and analyzed the plastomes of Lepismium cruciforme and Schlumbergera truncata, two South American epiphytic cacti. METHODS AND RESULTS: Our data reveal many gene losses in both plastomes and the first loss of functionality of the trnT-GGU gene in Cactaceae. The trnT-GGU is a pseudogene in L. cruciforme plastome and appears to be degenerating in the tribe Rhipsalideae. Although the plastome structure is conserved among the species of the tribe Rhipsalideae, with tribe-specific rearrangements, we mapped around 200 simple sequence repeats and identified nine nucleotide polymorphism hotspots, useful to improve the phylogenetic resolutions of the Rhipsalideae. Furthermore, our analysis indicated high gene divergence and rapid evolution of RNA editing sites in plastid protein-coding genes in Cactaceae. CONCLUSIONS: Our findings show that some characteristics of the Rhipsalideae tribe are conserved, such as plastome structure with IRs containing only the ycf2 and two tRNA genes, structural degeneration of the trnT-GGU gene and ndh complex, and lastly, pseudogenization of rpl33 and rpl23 genes, both plastid translation-related genes.

The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes.

MAIN CONCLUSION: The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.

Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.).

KEY MESSAGE: The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.

Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae).

MAIN CONCLUSION: Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.

Characterization of the complete plastid genome of Butia eriospatha (Arecaceae).

Butia eriospatha is an endemic palm species from the Atlantic Rainforest in Brazil, a biodiversity hotspot. This species is currently listed in the IUCN red list as vulnerable and lacks specific plastid markers for population genetics studies. In addition, the evolutionary relationship within the genus Butia is not yet well resolved. Here, we sequenced and characterized the complete plastid genome (plastome) sequence of B. eriospatha. The complete plastome sequence is 154,048 bp in length, with the typical quadripartite structure. This plastome length and genes content is consistent with other six species from tribe Cocoseae. However, the Inverted Repeat (IR) borders show some variation among the analyzed species from this tribe. Species from the Bactridinae (Astrocaryum and Acrocomia) and Elaeidinae (Elaeis) subtribes present the rps19 gene completely duplicated in the IR region. In contrast, all plastomes sequenced from the subtribe Attaleinae (Butia, Cocos, Syagrus) present one complete CDS of rps19 and one partial copy of rps19. The difference in the IR/LSC junctions between Attaleinae and the sister clades Bactridinae + Elaeidinae might be considered an evolutionary signal and the plastome sequence of B. eriopatha may be used in future studies of population genetics and phylogeny.

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

MAIN CONCLUSION: 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.

Genetic, evolutionary and phylogenetic aspects of the plastome of annatto (Bixa orellana L.), the Amazonian commercial species of natural dyes.

MAIN CONCLUSION: The plastome of B. orellana reveals specific evolutionary features, unique RNA editing sites, molecular markers and the position of Bixaceae within Malvales. Annatto (Bixa orellana L.) is a native species of tropical Americas with center of origin in Brazilian Amazonia. Its seeds accumulate the apocarotenoids, bixin and norbixin, which are only found in high content in this species. The seeds of B. orellana are commercially valued by the food industry because its dyes replace synthetic ones from the market due to potential carcinogenic risks. The increasing consumption of B. orellana seeds for dye extraction makes necessary the increase of productivity, which is possible accessing the genetic basis and searching for elite genotypes. The identification and characterization of molecular markers are essential to analyse the genetic diversity of natural populations and to establish suitable strategies for conservation, domestication, germplasm characterization and genetic breeding. Therefore, we sequenced and characterized in detail the plastome of B. orellana. The plastome of B. orellana is a circular DNA molecule of 159,708 bp with a typical quadripartite structure and 112 unique genes. Additionally, a total of 312 SSR loci were identified in the plastome of B. orellana. Moreover, we predicted in 23 genes a total of 57 RNA-editing sites of which 11 are unique for B. orellana. Furthermore, our plastid phylogenomic analyses, using the plastome sequences available in the plastid database belonging to species of order Malvales, indicate a closed relationship between Bixaceae and Malvaceae, which formed a sister group to Thymelaeaceae. Finally, our study provided useful data to be employed in several genetic and biotechnological approaches in B. orellana and related species of the family Bixaceae.

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae.

MAIN CONCLUSION: The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales.

KEY MESSAGE: The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.

An integrative overview of the molecular and physiological responses of sugarcane under drought conditions.

Drought is the main abiotic stress constraining sugarcane production. However, our limited understanding of the molecular mechanisms involved in the drought stress responses of sugarcane impairs the development of new technologies to increase sugarcane drought tolerance. Here, an integrated approach was performed to reveal the molecular and physiological changes in two closely related sugarcane cultivars, including the most extensively planted cultivar in Brazil (cv. RB867515), in response to moderate (-0.5 MPa) and severe (-1 MPa) drought stress at the transcriptional, translational, and posttranslational levels. The results show common and cultivar exclusive changes in specific genes related to photosynthesis, carbohydrate, amino acid, and phytohormone metabolism. The novel phosphoproteomics and redox proteomic analysis revealed the importance of posttranslational regulation mechanisms during sugarcane drought stress. The shift to soluble sugar, secondary metabolite production, and activation of ROS eliminating processes in response to drought tolerance were mechanisms exclusive to cv. RB867515, helping to explain the better performance and higher production of this cultivar under these stress conditions.

Mating System and Genetic Structure Across All Known Populations of Dyckia brevifolia: A Clonal, Endemic, and Endangered Rheophyte Bromeliad.

Dyckia brevifolia is an endemic rheophyte bromeliad that occurs exclusively in patches on rocky banks of the Itajaí-Açu River in southern Brazil. The genetic diversity of all known populations was carried out using allozyme markers and the total numbers of rosettes, reproductive rosettes, and clumps per population were characterized. The mating system was also investigated. Most rosettes were aggregated in groups, and the populations differed significantly in number of rosettes and reproductive rosettes per population. The outcrossing rate obtained was 8.2%, with predominant selfing. The populations presented an average of 1.4 alleles per locus and 27% of polymorphisms. The mean expected genetic diversity was 0.067. Downstream populations showed the highest genetic diversity which could be attributed to hydrochory (unidirectional river flow). Most genetic diversity is distributed among populations (F^ST = 0.402). Natural habitats of D. brevifolia are not recommended for the construction of hydroelectric plants given that it would seriously complicate in situ conservation of this species. Based on the results of this study, it can be concluded that between 35 and 161 reproductive rosettes must be collected for effective ex situ conservation, depending on the targeted population, or seeds collected from 157 seed-rosettes per population.

Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.

The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.

The contributions of wobbling and superwobbling to the reading of the genetic code.

Reduced bacterial genomes and most genomes of cell organelles (chloroplasts and mitochondria) do not encode the full set of 32 tRNA species required to read all triplets of the genetic code according to the conventional wobble rules. Superwobbling, in which a single tRNA species that contains a uridine in the wobble position of the anticodon reads an entire four-fold degenerate codon box, has been suggested as a possible mechanism for how tRNA sets can be reduced. However, the general feasibility of superwobbling and its efficiency in the various codon boxes have remained unknown. Here we report a complete experimental assessment of the decoding rules in a typical prokaryotic genetic system, the plastid genome. By constructing a large set of transplastomic knock-out mutants for pairs of isoaccepting tRNA species, we show that superwobbling occurs in all codon boxes where it is theoretically possible. Phenotypic characterization of the transplastomic mutant plants revealed that the efficiency of superwobbling varies in a codon box-dependent manner, but--contrary to previous suggestions--it is independent of the number of hydrogen bonds engaged in codon-anticodon interaction. Finally, our data provide experimental evidence of the minimum tRNA set comprising 25 tRNA species, a number lower than previously suggested. Our results demonstrate that all triplets with pyrimidines in third codon position are dually decoded: by a tRNA species utilizing standard base pairing or wobbling and by a second tRNA species employing superwobbling. This has important implications for the interpretation of the genetic code and will aid the construction of synthetic genomes with a minimum-size translational apparatus.

Engineering plastid fatty acid biosynthesis to improve food quality and biofuel production in higher plants.

The ability to manipulate plant fatty acid biosynthesis by using new biotechnological approaches has allowed the production of transgenic plants with unusual fatty acid profile and increased oil content. This review focuses on the production of very long chain polyunsaturated fatty acids (VLCPUFAs) and the increase in oil content in plants using molecular biology tools. Evidences suggest that regular consumption of food rich in VLCPUFAs has multiple positive health benefits. Alternative sources of these nutritional fatty acids are found in cold-water fishes. However, fish stocks are in severe decline because of decades of overfishing, and also fish oils can be contaminated by the accumulation of toxic compounds. Recently, there is also an increase in oilseed use for the production of biofuels. This tendency is partly associated with the rapidly rising costs of petroleum, increased concern about the environmental impact of fossil oil and the attractive need to develop renewable sources of fuel. In contrast to this scenario, oil derived from crop plants is normally contaminant free and less environmentally aggressive. Genetic engineering of the plastid genome (plastome) offers a number of attractive advantages, including high-level foreign protein expression, marker-gene excision and transgene containment because of maternal inheritance of plastid genome in most crops. Here, we describe the possibility to improve fatty acid biosynthesis in plastids, production of new fatty acids and increase their content in plants by genetic engineering of plastid fatty acid biosynthesis via plastid transformation.

Phylogeography of plastid DNA sequences suggests post-glacial southward demographic expansion and the existence of several glacial refugia for Araucaria angustifolia.

Despite the high diversity of the Southern South American environments, the patterns and processes driving both their species diversity and demographic history are still poorly known and are a challenging task. In this study, we evaluate plastid DNA sequences of the conifer species Araucaria angustifolia aiming to (i) assess the species genetic structure within its main range of occurrence, (ii) infer its population demographic history, looking for evidence of southward expansion, (iii) search for evidence of glacial refugia within the species distribution area and (iv) discuss some conservation and management strategies for this species. Twenty haplotypes were identified, revealing the presence of three distinct genetic groups across the geographic range of the species and structuring the populations into Northern, Central and Southern groups. Our results suggest the occurrence of post-glacial expansion of A. angustifolia towards the south, as well as the existence of at least three refugia within the species occurrence area. Testing the occurrence of historical demographic expansion, we suggest that genetic groups experienced fluctuations in effective size, associated to a structured distribution of populations. The identification of three genetic groups in this study corroborates the proposition of using the geographic distribution of A. angustifolia for selecting in situ conservation areas, for planning seed collection for ex situ conservation, as well as for the delineation of seed zones.

Tobacco plastid ribosomal protein S18 is essential for cell survival.

Plastid genomes contain a conserved set of genes most of which are involved in either photosynthesis or gene expression. Among the ribosomal protein genes present in higher plant plastid genomes, rps18 is special in that it is absent from the plastid genomes of several non-green unicellular organisms, including Euglena longa and Toxoplasma gondii. Here we have tested whether the ribosomal protein S18 is required for translation by deleting the rps18 gene from the tobacco plastid genome. We report that, while deletion of the rps18 gene was readily obtained, no homoplasmic Deltarps18 plants or leaf sectors could be isolated. Instead, segregation into homoplasmy led to severe defects in leaf development suggesting that the knockout of rps18 is lethal and the S18 protein is required for cell survival. Our data demonstrate that S18 is indispensable for plastid ribosome function in tobacco and support an essential role for plastid translation in plant development. Moreover, we demonstrate the occurrence of flip-flop recombination on short inverted repeat sequences which generates different isoforms of the transformed plastid genome that differ in the orientation a 70 kb segment in the large single-copy region. However, infrequent occurrence of flip-flop recombination and random segregation of plastid genomes result in the predominant presence of only one of the isoforms in many tissue samples. Implications for the interpretation of chloroplast transformation experiments and vector design are discussed.

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.

Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology.

During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.

An improved protocol for intact chloroplasts and cpDNA isolation in conifers.

BACKGROUND: Performing chloroplast DNA (cpDNA) isolation is considered a major challenge among different plant groups, especially conifers. Isolating chloroplasts in conifers by such conventional methods as sucrose gradient and high salt has not been successful. So far, plastid genome sequencing protocols for conifer species have been based mainly on long-range PCR, which is known to be time-consuming and difficult to implement. METHODOLOGY/PRINCIPAL FINDINGS: We developed a protocol for cpDNA isolation using three different conifer families: Araucaria angustifolia and Araucaria bidwilli (Araucariaceae), Podocarpus lambertii (Podocarpaceae) and Pinus patula (Pinaceae). The present protocol is based on high salt isolation buffer followed by saline Percoll gradient. Combining these two strategies allowed enhanced chloroplast isolation, along with decreased contamination caused by polysaccharides, polyphenols, proteins, and nuclear DNA in cpDNA. Microscopy images confirmed the presence of intact chloroplasts in high abundance. This method was applied to cpDNA isolation and subsequent sequencing by Illumina MiSeq (2×250 bp), using only 50 ng of cpDNA. Reference-guided chloroplast genome mapping showed that high average coverage was achieved for all evaluated species: 24.63 for A. angustifolia, 135.97 for A. bidwilli, 1196.10 for P. lambertii, and 64.68 for P. patula. CONCLUSION: Results show that this improved protocol is suitable for enhanced quality and yield of chloroplasts and cpDNA isolation from conifers, providing a useful tool for studies that require isolated chloroplasts and/or whole cpDNA sequences.