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

Neotropical palms: from their conservation to economic potential

Palms (Arecaceae) are an important group of plants widely distributed throughout the world. The Arecaceae family comprises a great diversity of species, however, many of them are threatened with extinction due to their unbridled exploitation in search of economically important resources. An overview of palms biology will be presented, with emphasis on genetics and genomic resources of several species, as well as their socioeconomic impact worldwide, highlighting the main advances in recent research. Our discussion also covers the demand for urgent measures toward conservation and preservation of palms since they play key roles in maintaining biodiversity and providing essential ecosystem services. Fundamentally, this article is to raise awareness about the importance of palms and to encourage the protection and conservation of these valuable species.

Training set optimization is a feasible alternative for perennial orphan crop domestication and germplasm management: an Acrocomia aculeata example

Orphan perennial native species are gaining importance as sustainability in agriculture becomes crucial to mitigate climate change. Nevertheless, issues related to the undomesticated status and lack of improved germplasm impede the evolution of formal agricultural initiatives. Acrocomia aculeata - a neotropical palm with potential for oil production - is an example. Breeding efforts can aid the species to reach its full potential and increase market competitiveness. Here, we present genomic information and training set optimization as alternatives to boost orphan perennial native species breeding using Acrocomia aculeata as an example. Furthermore, we compared three SNP calling methods and, for the first time, presented the prediction accuracies of three yield-related traits. We collected data for two years from 201 wild individuals. These trees were genotyped, and three references were used for SNP calling: the oil palm genome, de novo sequencing, and the A. aculeata transcriptome. The traits analyzed were fruit dry mass (FDM), pulp dry mass (PDM), and pulp oil content (OC). We compared the predictive ability of GBLUP and BayesB models in cross- and real validation procedures. Afterwards, we tested several optimization criteria regarding consistency and the ability to provide the optimized training set that yielded less risk in both targeted and untargeted scenarios. Using the oil palm genome as a reference and GBLUP models had better results for the genomic prediction of FDM, OC, and PDM (prediction accuracies of 0.46, 0.45, and 0.39, respectively). Using the criteria PEV, r-score and core collection methodology provides risk-averse decisions. Training set optimization is an alternative to improve decision-making while leveraging genomic information as a cost-saving tool to accelerate plant domestication and breeding. The optimized training set can be used as a reference for the characterization of native species populations, aiding in decisions involving germplasm collection and construction of breeding populations.

The complete chloroplast genome of Rhododendronambiguum and comparative genomics of related species

Rhododendron Linnaeus, 1753, the largest genus of woody plants in the Northern Hemisphere, includes some of the most significant species in horticulture. Rhododendronambiguum Hemsl, 1911, a member of subsection Triflora Sleumer 1947, exemplifies typical alpine Rhododendron species. The analysis of the complete chloroplast genome of R.ambiguum offers new insights into the evolution of Rhododendron species and enhances the resolution of phylogenetic relationships. This genome is composed of 207,478 base pairs, including a pair of inverted repeats (IRs) of 47,249 bp each, separated by a large single-copy (LSC) region of 110,367 bp and a small single-copy (SSC) region of 2,613 bp. It contains 110 genes: 77 protein-coding genes, 29 tRNAs, four unique rRNAs (4.5S, 5S, 16S, and 23S), with 16 genes duplicated in the IRs. Comparative analyses reveal substantial diversity in the Rhododendron chloroplast genome structures, identifying a fourth variant pattern. Specifically, four highly divergent regions (trnI-rpoB, ndhE-psaC, rpl32-ndhF, rrn16S-trnI) were noted in the intergenic spacers. Additionally, 76 simple sequence repeats were identified. Positive selection signals were detected in four genes (cemA, rps4, rpl16, and rpl14), evidenced by high Ka/Ks ratios. Phylogenetic reconstruction based on two datasets (shared protein-coding genes and complete chloroplast genomes) suggests that R.ambiguum is closely related to R.concinnum Hemsley, 1889. However, the phylogenetic positions of subsection Triflora Pojarkova, 1952 species remain unresolved, indicating that the use of complete chloroplast genomes for phylogenetic research in Rhododendron requires careful consideration. Overall, our findings provide valuable genetic information that will enhance understanding of the evolution, molecular biology, and genetic improvement of Rhododendron spieces.

Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

Magnoliaceae plants are industrial tree species with high ornamental and medicinal value. We published six complete chloroplast genomes of Magnoliaceae by using Illumina sequencing. These showed a typical quadripartite structure of angiosperm and were 159,901−160,008 bp in size. A total of 324 microsatellite loci and six variable intergenic regions (Pi > 0.01) were identified in six genomes. Compared with five other genomes, the contraction and expansion of the IR regions were significantly different in Manglietia grandis. To gain a more thorough understanding of the intergeneric relationships in Magnoliaceae, we also included 31 published chloroplast genomes of close relative species for phylogenetic analyses. New insights into the intergeneric relationships of Magnoliaceae are provided based on our results and previous morphological, phytochemical and anatomical information. We suggest that the genus Yulania should be separated from the genus Michelia and its systematic position of should be restored; the genera Paramichelia and Tsoongiodendron should be merged into the genus Michelia; the genera Pachylarnax and Parakmeria should be combined into one genus. These findings will provide a theoretical basis for adjusting the phylogenetic position of Magnoliaceae at the molecular level.

Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis

Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (F_ST = 0.77), especially between E. edulis and E. precatoria (F_ST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.

Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species

Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium.

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

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.

Structural and evolutive features of the Plinia phitrantha and P. cauliflora plastid genomes and evolutionary relationships within tribe Myrteae (Myrtaceae)

Plinia phitrantha and P. cauliflora are Myrtaceae species with recognized horticultural and pharmacological potential. Nevertheless, studies on molecular genetics and the evolution of these species are absent in the literature. In this study, we report the complete plastid genome sequence of these species and an analysis of structural and evolutive features of the plastid genome within the tribe Myrteae. The two plastid genomes present the conserved quadripartite structure and are similar to already reported plastid genomes of Myrteae species concerning the size, number, and order of the genes. A total of 69-70 SSR loci, 353 single nucleotide polymorphisms, and 574 indels were identified in P. phitrantha and P. caulifora. Observed evolutive features of the plastid genomes support the development of programs for the conservation and breeding of Plinia. The phylogenomic analysis based on the complete plastid genome sequence of 15 Myrteae species presented a robust phylogenetic signal and evolutive traits of the tribe. Ten hotspots of nucleotide diversity were identified, evidence of purifying selection was observed in 27 genes, and relative conservation of the plastid genomes was confirmed for Myrteae. Altogether, the outcomes of the present study provide support for planning conservation, breeding, and biotechnological programs for Plinia species.

Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae

BACKGROUND

The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae.

RESULTS

The chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species.

CONCLUSION

Orchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124-156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103-158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76-103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.

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

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.

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

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.

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

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.

Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene

Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing ‘hotspots’ of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as ‘hotspots’ of variability, and (iii) the genes identified as ‘hotspots’ of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.

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.

Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)

BACKGROUND

Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P. japonica remains poorly understood.

RESULTS

We used next-generation sequencing to generate complete plastomes of P. japonica, P. verticillata, Trillium govanianum, Ypsilandra thibetica and Y. yunnanensis. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in Paris were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant Paris and Trillium occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between P. japonica and the section Euthyra was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia.

CONCLUSIONS

The genome size expansion in the most recent common ancestor for Paris and Trillium was most possibly a gradual process that lasted for approximately 20 million years. The divergence of P. japonica (section Kinugasa) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in P. japonica. Moreover, our results support the taxonomic treatment of Paris as a genus rather than dividing it into three genera, but do not support the recognition of T. govanianum as the separate genus Trillidium.

The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data

Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification-refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae.

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

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.

Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species

BACKGROUND

The macaúba palm is a novel feedstock for oil production suitable for multiple uses, including as biodiesel and in the food and cosmetic industries. As an efficient alternative, the macaúba palm has limited genomic resources, particularly expressed sequence tag (EST) markers. We report a comprehensive set of validated EST-simple sequence repeat (SSR) markers by using transcriptome sequencing, its application in genetic diversity analysis and cross transferability in other palm trees with environmental and economic importance.

RESULTS

In this study, a total of 418 EST-SSRs were identified to be unique for one transcript and region; 232 EST-SSRs were selected, with trinucleotide repeats being the most frequent motif, representing 380 (90.9%), followed by composited (4.5%), di- (3.6%), and hexanucleotides (3.6%). A total of 145 EST-SSRs (62.5%) were validated for consistent amplification in seventeen macaúba palm samples, and 100 were determined to be polymorphic with PIC values ranging from 0.25 to 0.77. Genetic diversity analysis was performed with the 20 most informative EST-SSR markers showing a distinct separation of the different groups of macaúba palm. Additionally, these 145 markers were transferred in six other palm species resulting in transferability rates of 99% (144) in Acrocomia intumescens, 98% (143) in Acrocomia totai, 80.7% (117 EST-EST) in African oil palm (Elaeis guineensis) and peach palm (Bactris gasipaes) samples, 70% (102) in the juçara palm (Euterpe edulis) and 71.7% (104) in the hat palm (Sabal causiarum). Analysis of genetic distance showed a high separation in accordance with geographic location, establishing distinct groups by genera.

CONCLUSIONS

The EST markers identified in our study are a valuable resource and provide a genomic tool for genetic mapping and further genetic studies, as well as evaluation of co-location between QTLs and functionally associated markers.

The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.

The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids

Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus.

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.