Persea americana (avocado): bringing ancient flowers to fruit in the genomics era

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world's avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.

Avocado Seeds Relieve Oxidative Stress-Dependent Nephrotoxicity but Enhance Immunosuppression Induced by Cyclosporine in Rats

Cyclosporine A's (CsA) immunosuppressive effect makes it an ideal drug for organ transplantation. However, CsA's uses are restricted due to its side effects. We investigated the effects of avocado seed (AvS) powder on CsA-induced nephrotoxicity and immunosuppression in rats. The injection of CsA (5 mg/kg, subcutaneously, for 10 days) increased serum levels of creatinine, uric acid, and urea, and the renal levels of the malondialdehyde. It decreased creatinine clearance and the renal activity of antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase) and Na⁺/K⁺ ATPase. The administration of CsA also significantly downregulated the renal expression of interferon-gamma, tumor necrosis factor-alpha, interleukin 1 beta, monocyte chemotactic protein 1, intercellular adhesion molecule-1, and vascular cell adhesion molecule 1 genes, and increased renal DNA damage. Histopathological examination confirmed the biochemical and molecular alterations that accompanied CsA nephrotoxicity. All CsA-induced deleterious effects, except immunosuppression, were ameliorated by feeding rats on a basal diet supplemented with 5% AvS powder for 4 weeks. Importantly, AvS also maximized CsA's immunosuppressive effect. These findings suggest a potential ameliorative effect of AvS on CsA-induced nephrotoxicity, and AvS enhances CsA's immunosuppressive effect. Therefore, AvS might be used in combination with CsA in transplantation treatment to relieve the CsA-induced nephrotoxicity.

Functional and Predictive Structural Characterization of WRINKLED2, A Unique Oil Biosynthesis Regulator in Avocado

WRINKLED1 (WRI1), a member of the APETALA2 (AP2) class of transcription factors regulates fatty acid biosynthesis and triacylglycerol (TAG) accumulation in plants. Among the four known Arabidopsis WRI1 paralogs, only WRI2 was unable to complement and restore fatty acid content in wri1-1 mutant seeds. Avocado (Persea americana) mesocarp, which accumulates 60-70% dry weight oil content, showed high expression levels for orthologs of WRI2, along with WRI1 and WRI3, during fruit development. While the role of WRI1 as a master regulator of oil biosynthesis is well-established, the function of WRI1 paralogs is poorly understood. Comprehensive and comparative in silico analyses of WRI1 paralogs from avocado (a basal angiosperm) with higher angiosperms Arabidopsis (dicot), maize (monocot) revealed distinct features. Predictive structural analyses of the WRI orthologs from these three species revealed the presence of AP2 domains and other highly conserved features, such as intrinsically disordered regions associated with predicted PEST motifs and phosphorylation sites. Additionally, avocado WRI proteins also contained distinct features that were absent in the nonfunctional Arabidopsis ortholog AtWRI2. Through transient expression assays, we demonstrated that both avocado WRI1 and WRI2 are functional and drive TAG accumulation in Nicotiana benthamiana leaves. We predict that the unique features and activities of ancestral PaWRI2 were likely lost in orthologous genes such as AtWRI2 during evolution and speciation, leading to at least partial loss of function in some higher eudicots. This study provides us with new targets to enhance oil biosynthesis in plants.

Advances in Understanding Defense Mechanisms in Persea americana Against Phytophthora cinnamomi

Avocado (Persea americana) is an economically important fruit crop world-wide, the production of which is challenged by notable root pathogens such as Phytophthora cinnamomi and Rosellinia necatrix. Arguably the most prevalent, P. cinnamomi, is a hemibiotrophic oomycete which causes Phytophthora root rot, leading to reduced yields and eventual tree death. Despite its' importance, the development of molecular tools and resources have been historically limited, prohibiting significant progress toward understanding this important host-pathogen interaction. The development of a nested qPCR assay capable of quantifying P. cinnamomi during avocado infection has enabled us to distinguish avocado rootstocks as either resistant or tolerant - an important distinction when unraveling the defense response. This review will provide an overview of our current knowledge on the molecular defense pathways utilized in resistant avocado rootstock against P. cinnamomi. Notably, avocado demonstrates a biphasic phytohormone profile in response to P. cinnamomi infection which allows for the timely expression of pathogenesis-related genes via the NPR1 defense response pathway. Cell wall modification via callose deposition and lignification have also been implicated in the resistant response. Recent advances such as composite plant transformation, single nucleotide polymorphism (SNP) analyses as well as genomics and transcriptomics will complement existing molecular, histological, and biochemical assay studies and further elucidate avocado defense mechanisms.

Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.

The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

The avocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings and the admixed nature of Hass and provide a look at how pathogen interactions have shaped the avocado’s more recent genomic evolutionary history.

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.

Primary Metabolism in Avocado Fruit

Avocado (Persea americana Mill) is rich in a variety of essential nutrients and phytochemicals; thus, consumption has drastically increased in the last 10 years. Avocado unlike other fruit is characterized by oil accumulation during growth and development and presents a unique carbohydrate pattern. There are few previous and current studies related to primary metabolism. The fruit is also quite unique since it contains large amounts of C7 sugars (mannoheptulose and perseitol) acting as transportable and storage sugars and as potential regulators of fruit ripening. These C7 sugars play a central role during fruit growth and development, but still confirmation is needed regarding the biosynthetic routes and the physiological function during growth and development of avocado fruit. Relatively recent transcriptome studies on avocado mesocarp during development and ripening have revealed that most of the oil is synthesized during early stages of development and that oil synthesis is halted when the fruit is harvested (pre-climacteric stage). Most of the oil is accumulated in the form of triacylglycerol (TAG) representing 60-70% in dry basis of the mesocarp tissue. During early stages of fruit development, high expression of transcripts related to fatty acid and TAG biosynthesis has been reported and downregulation of same genes in more advanced stages but without cessation of the process until harvest. The increased expression of fatty acid key genes and regulators such as PaWRI1, PaACP4-2, and PapPK-β-1 has also been reported to be consistent with the total fatty acid increase and fatty acid composition during avocado fruit development. During postharvest, there is minimal change in the fatty acid composition of the fruit. Almost inexistent information regarding the role of organic acid and amino acid metabolism during growth, development, and ripening of avocado is available. Cell wall metabolism understanding in avocado, even though crucial in terms of fruit quality, still presents severe gaps regarding the interactions between cell wall remodeling, fruit development, and postharvest modifications.

Chemical Profile and Safety Assessment of a Food-Grade Acetogenin-Enriched Antimicrobial Extract from Avocado Seed

Acetogenins are bioactive fatty acid derivatives found in avocado tissues. Their efficacy as antimicrobials has been documented and initiated interest to use them as replacements of synthetic food additives. The present work focused on evaluation of multiple analytical methodologies for detection and quantification of organic solids present in a food-grade acetogenin-enriched extract (Avosafe®), and on its safety evaluations using bacterial reverse mutation (AMES) tests and acute oral toxicity to rat assays. Results confirmed chemical structures of two acetogenins as present in Avosafe® (AcO-avocadyne-(0) and AcO-avocadiene B-(3)), and together with seven other previously known compounds, quantified 94.74 ± 5.77% w/w of its solids as acetogenins. Safety evaluations indicated that Avosafe® was non-mutagenic and had an acute median lethal oral dose (LD50) to rats higher than the maximum concentration tested (>2000 mg·kg-1), with no signs of macroscopic abnormalities in organs. Mean body weight and hematological and biochemical parameters were normal after 14 days of a single oral dose of 2000 mg·kg-1. The results advance scientific information on the safety of avocado seed acetogenins and also generate new knowledge on profiles and concentrations of individual acetogenins found in avocado tissues (seed, pulp, and leaves) and in Avosafe®.

Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.

De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development

BACKGROUND

Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar 'Hass' especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of 'Hass' fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest).

RESULTS

The 'Hass' de novo transcriptome contains 62,203 contigs (x̅=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate ≤ 0.01) found 8672 genes considering all developmental stages. From this analysis, genes were clustered according to their expression pattern and 1209 genes show correlation with the four developmental stages.

CONCLUSIONS

Candidate genes are proposed as possible biomarkers for monitoring the development of the 'Hass' avocado fruit associated with lipid metabolism, ethylene signaling pathway, auxin signaling pathway, and components of the cell wall.

Polyphenolic Profile and Antioxidant Activity of Leaf Purified Hydroalcoholic Extracts from Seven Mexican Persea americana Cultivars

Persea americana (avocado) is a fruit consumed worldwide; however, since avocado leaves are apparently a natural ingredient that can be used as a traditional medicine, they can be a potential source of bioactive compounds. This study aimed to analyze the antioxidant activity of seven Mexican avocado leaf extracts by DPPH^•, ABTS^•+, and lipid peroxidation (LPO), and to identify the compound profile by liquid chromatography coupled to mass spectrometry/electron spray ionization. The highest free radical-scavenging activity was observed for Platano Delgado and Criollo 6 avocado cultivars havin IC₅₀ values of 271.86 ± 13.69 and 269.56 ± 6.53 for DPPH^• and ABTS^•+ radicals, respectively, while the best result for lipid oxidation inhibition was registered in Criollo 6 cultivar extract. In this study forty-one compounds were detected in avocado leaves of the the seven cultivars analyzed, and of these compounds, eighteen phenolics were identified for first time in such plant material. The present study demonstrated that Mexican cultivars of Persea americana possess diverse polyphenolic compounds with strong antioxidant activity, which might be useful in the food and pharmaceutical industries.

The transition from somatic to germline identity shows conserved and specialized features during angiosperm evolution

How and why specific plant cells adopt germline identity during ovule development has proved challenging to address, and the pathways that are active in the ovules of basal/early-divergent angiosperms possessing a multilayered nucellus are still unclear. Here, we compare megasporogenesis between two early-divergent angiosperms (Annona cherimola and Persea americana) and the evolutionarily derived Arabidopsis thaliana, studying the three-dimensional spatial position of the megaspore mother cell (MMC), the compositional details of the MMC wall and the location of PIN1 expression. Specific wall polymers distinguished the central position of the MMC and its meiotic products from surrounding tissues in early-divergent angiosperms, whereas, in A. thaliana, only callose (in mature MMCs) and arabinogalactan proteins (AGPs) (in megaspores) distinguished the germline. However, PIN1 expression, which regulates polar auxin transport, was observed around the MMC in the single-layer nucellus of A. thaliana and in the multilayered nucellus of A. cherimola, or close to the MMC in P. americana. The data reveal a similar microenvironment in relation to auxin during megasporogenesis in all three species. However, the different wall polymers that mark MMC fate in early-divergent angiosperms may reflect a specific response to mechanical stress during differentiation, or the specific recruitment of polymers to sustain MMC growth.

Transcriptome Analysis of Cell Wall and NAC Domain Transcription Factor Genes during Elaeis guineensis Fruit Ripening: Evidence for Widespread Conservation within Monocot and Eudicot Lineages

The oil palm (Elaeis guineensis), a monocotyledonous species in the family Arecaceae, has an extraordinarily oil rich fleshy mesocarp, and presents an original model to examine the ripening processes and regulation in this particular monocot fruit. Histochemical analysis and cell parameter measurements revealed cell wall and middle lamella expansion and degradation during ripening and in response to ethylene. Cell wall related transcript profiles suggest a transition from synthesis to degradation is under transcriptional control during ripening, in particular a switch from cellulose, hemicellulose, and pectin synthesis to hydrolysis and degradation. The data provide evidence for the transcriptional activation of expansin, polygalacturonase, mannosidase, beta-galactosidase, and xyloglucan endotransglucosylase/hydrolase proteins in the ripening oil palm mesocarp, suggesting widespread conservation of these activities during ripening for monocotyledonous and eudicotyledonous fruit types. Profiling of the most abundant oil palm polygalacturonase (EgPG4) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) transcripts during development and in response to ethylene demonstrated both are sensitive markers of ethylene production and inducible gene expression during mesocarp ripening, and provide evidence for a conserved regulatory module between ethylene and cell wall pectin degradation. A comprehensive analysis of NAC transcription factors confirmed at least 10 transcripts from diverse NAC domain clades are expressed in the mesocarp during ripening, four of which are induced by ethylene treatment, with the two most inducible (EgNAC6 and EgNAC7) phylogenetically similar to the tomato NAC-NOR master-ripening regulator. Overall, the results provide evidence that despite the phylogenetic distance of the oil palm within the family Arecaceae from the most extensively studied monocot banana fruit, it appears ripening of divergent monocot and eudicot fruit lineages are regulated by evolutionarily conserved molecular physiological processes.

Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico

Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]. Deviation from Hardy Weinberg Equilibrium and high inter-locus linkage disequilibrium were observed especially in drymifolia, and guatemalensis. Total averages of the observed and expected heterozygosity were 0.59 and 0.75, respectively. Although clear genetic differentiation was not observed among 3 botanical races: americana, drymifolia, and guatemalensis, the analyzed Mexican population can be classified into two groups that correspond to two different ecological regions. We developed a core-collection by K-means clustering method. The selected 36 individuals as core-collection successfully represented more than 80% of total alleles and showed heterozygosity values equal to or higher than those of the original collection, despite its constituting slightly more than 10% of the latter. Accessions selected as members of the core collection have now become candidates to be introduced in cryopreservation implying a minimum loss of genetic diversity and a back-up for existing field collections of such important genetic resources.

Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era

The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems,Arabidopsis thalianaandAntirrhinum majus Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of "model clades" for genomic and evolutionary-developmental analyses, instead of the primary use of single "model organisms." We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.

Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp

BACKGROUND

The mechanism by which plants synthesize and store high amounts of triacylglycerols (TAG) in tissues other than seeds is not well understood. The comprehension of controls for carbon partitioning and oil accumulation in nonseed tissues is essential to generate oil-rich biomass in perennial bioenergy crops. Persea americana (avocado), a basal angiosperm with unique features that are ancestral to most flowering plants, stores ~ 70 % TAG per dry weight in its mesocarp, a nonseed tissue. Transcriptome analyses of select pathways, from generation of pyruvate and leading up to TAG accumulation, in mesocarp tissues of avocado was conducted and compared with that of oil-rich monocot (oil palm) and dicot (rapeseed and castor) tissues to identify tissue- and species-specific regulation and biosynthesis of TAG in plants.

RESULTS

RNA-Seq analyses of select lipid metabolic pathways of avocado mesocarp revealed patterns similar to that of other oil-rich species. However, only some predominant orthologs of the fatty acid biosynthetic pathway genes in this basal angiosperm were similar to those of monocots and dicots. The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development. Gene expression levels for enzymes involved in terminal steps to TAG biosynthesis in the ER further indicated that both acyl-CoA-dependent and -independent mechanisms might play a role in TAG assembly, depending on the developmental stage of the fruit. Furthermore, in addition to the expression of an ortholog of WRINKLED1 (WRI1), a regulator of fatty acid biosynthesis, high transcript levels for WRI2-like and WRI3-like suggest a role for additional transcription factors in nonseed oil accumulation. Plastid pyruvate necessary for fatty acid synthesis is likely driven by the upregulation of genes involved in glycolysis and transport of its intermediates. Together, a comparative transcriptome analyses for storage oil biosynthesis in diverse plants and tissues suggested that several distinct and conserved features in this basal angiosperm species might contribute towards its rich TAG content.

CONCLUSIONS

Our work represents a comprehensive transcriptome resource for a basal angiosperm species and provides insight into their lipid metabolism in mesocarp tissues. Furthermore, comparison of the transcriptome of oil-rich mesocarp of avocado, with oil-rich seed and nonseed tissues of monocot and dicot species, revealed lipid gene orthologs that are highly conserved during evolution. The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified. This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp

BACKGROUND

The mechanism by which plants synthesize and store high amounts of triacylglycerols (TAG) in tissues other than seeds is not well understood. The comprehension of controls for carbon partitioning and oil accumulation in nonseed tissues is essential to generate oil-rich biomass in perennial bioenergy crops. Persea americana (avocado), a basal angiosperm with unique features that are ancestral to most flowering plants, stores ~ 70 % TAG per dry weight in its mesocarp, a nonseed tissue. Transcriptome analyses of select pathways, from generation of pyruvate and leading up to TAG accumulation, in mesocarp tissues of avocado was conducted and compared with that of oil-rich monocot (oil palm) and dicot (rapeseed and castor) tissues to identify tissue- and species-specific regulation and biosynthesis of TAG in plants.

RESULTS

RNA-Seq analyses of select lipid metabolic pathways of avocado mesocarp revealed patterns similar to that of other oil-rich species. However, only some predominant orthologs of the fatty acid biosynthetic pathway genes in this basal angiosperm were similar to those of monocots and dicots. The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development. Gene expression levels for enzymes involved in terminal steps to TAG biosynthesis in the ER further indicated that both acyl-CoA-dependent and -independent mechanisms might play a role in TAG assembly, depending on the developmental stage of the fruit. Furthermore, in addition to the expression of an ortholog of WRINKLED1 (WRI1), a regulator of fatty acid biosynthesis, high transcript levels for WRI2-like and WRI3-like suggest a role for additional transcription factors in nonseed oil accumulation. Plastid pyruvate necessary for fatty acid synthesis is likely driven by the upregulation of genes involved in glycolysis and transport of its intermediates. Together, a comparative transcriptome analyses for storage oil biosynthesis in diverse plants and tissues suggested that several distinct and conserved features in this basal angiosperm species might contribute towards its rich TAG content.

CONCLUSIONS

Our work represents a comprehensive transcriptome resource for a basal angiosperm species and provides insight into their lipid metabolism in mesocarp tissues. Furthermore, comparison of the transcriptome of oil-rich mesocarp of avocado, with oil-rich seed and nonseed tissues of monocot and dicot species, revealed lipid gene orthologs that are highly conserved during evolution. The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified. This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids

BACKGROUND

Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information.

RESULTS

The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening.

CONCLUSIONS

A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.

Analysis of expressed sequence tags (ESTs) from avocado seed (Persea americana var. drymifolia) reveals abundant expression of the gene encoding the antimicrobial peptide snakin

Avocado is one of the most important fruits in the world. Avocado "native mexicano" (Persea americana var. drymifolia) seeds are widely used in the propagation of this plant and are the primary source of rootstocks globally for a variety of avocado cultivars, such as the Hass avocado. Here, we report the isolation of 5005 ESTs from the 5' ends of P. americana var. drymifolia seed cDNA clones representing 1584 possible unigenes. These avocado seed ESTs were compared with the avocado flower EST library, and we detected several genes that are expressed either in both tissues or only in the seed. The snakin gene, which encodes an element of the innate immune response in plants, was one of those most frequently found among the seed ESTs, and this suggests that it is abundantly expressed in the avocado seed. We expressed the snakin gene in a heterologous system, namely the bovine endothelial cell line BVE-E6E7. Conditioned media from transfected BVE-E6E7 cells showed antimicrobial activity against strains of Escherichia coli and Staphylococcus aureus. This is the first study of the function of the snakin gene in plant seed tissue, and our observations suggest that this gene might play a protective role in the avocado seed.

EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi

BACKGROUND

Avocado (Persea americana) belongs to the Lauraceae family and is an important commercial fruit crop in over 50 countries. The most serious pathogen affecting avocado production is Phytophthora cinnamomi which causes Phytophthora root rot (PRR). Root pathogens such as P. cinnamomi and their interactions with hosts are poorly understood and despite the importance of both the avocado crop and the effect Phytophthora has on its cultivation, there is a lack of molecular knowledge underpinning our understanding of defence strategies against the pathogen. In order to initiate a better understanding of host-specific defence we have generated EST data using 454 pyrosequencing and profiled nine defence-related genes from Pc-infected avocado roots.

RESULTS

2.0 Mb of data was generated consisting of ~10,000 reads on a single lane of the GS FLX platform. Using the Newbler assembler 371 contigs were assembled, of which 367 are novel for Persea americana. Genes were classified according to Gene Ontology terms. In addition to identifying root-specific ESTs we were also able to identify and quantify the expression of nine defence-related genes that were differentially regulated in response to P. cinnamomi. Genes such as metallothionein, thaumatin and the pathogenesis related PsemI, mlo and profilin were found to be differentially regulated.

CONCLUSIONS

This is the first study in elucidating the avocado root transcriptome as well as identifying defence responses of avocado roots to the root pathogen P. cinnamomi. Our data is currently the only EST data that has been generated for avocado rootstocks, and the ESTs identified in this study have already been useful in identifying defence-related genes as well as providing gene information for other studies looking at processes such as ROS regulation as well as hypoxia in avocado roots. Our EST data will aid in the elucidation of the avocado transcriptome and identification of markers for improved rootstock breeding and screening. The characterization of the avocado transcriptome will furthermore form a basis for functional genomics of basal angiosperms.

A proposed conserved role for an avocado FW2.2-like gene as a negative regulator of fruit cell division

Previous studies using 'Hass' avocado and its small fruit (SF) phenotype as a model showed that SF is limited by cell number, not by cell size. In an attempt to explore the molecular mechanisms regulating avocado fruit cell division, we isolated four distinct avocado cell proliferation-related genes and investigated their expression characteristics, comparing normal fruit (NF) and SF developmental patterns. Three cDNAs termed PaCYCA1, PaCYCB1 and PaPCNA, encoding two mitotic cyclins and a proliferating cell nuclear antigen (PCNA), were first isolated from young NF tissues. The accumulation of their transcripts was predominant in mitotically active organs, including young fruitlets, leaves and roots. Furthermore, a fourth full-length cDNA, designated Pafw2.2-like, encoding a FW2.2 (fruit-weight)-like protein, was isolated from SF tissues. FW2.2 is postulated to function as a negative regulator of cell division in tomato fruit. Remarkably, northern analysis revealed that the accumulation of the mitotic cyclins and of PCNA transcripts gradually decreased in NF tissues during growth, whereas in SF, their levels had already decreased at earlier stages of fruit development, concomitant with an earlier arrest of fruit cell division activity. In contrast, parallel sq-RT-PCR analysis showed that Pafw2.2-like mRNA accumulation was considerably higher in SF tissues than in the same NF tissues essentially at all examined stages of fruit growth. Together, our data suggest essential roles for the two mitotic cyclins genes and the PCNA gene in regulating avocado fruit development. Furthermore, the possibility that Pafw2.2-like acts as does fw2.2 in tomato, is discussed.

Antimicrobial activity of crude epicarp and seed extracts from mature avocado fruit (Persea americana) of three cultivars

The epicarp and seed of Persea Americana Mill. var. Hass (Lauraceae), Persea Americana Mill. var. Shepard, and Persea americana Mill. var Fuerte cultivars of mature avocados (n = 3) were ground separately and extracted with both absolute ethanol and distilled water. Extracts were analyzed for antimicrobial activity using the microtiter broth microdilution assay against four Gram-positive bacteria, six Gram-negative bacteria, and one yeast. Antimicrobial activity against two molds was determined by the hole plate method. The ethanol extracts showed antimicrobial activity (104.2-416.7 microg/mL) toward both Gram-positive and Gram-negative bacteria (except Escherichia coli), while inhibition of the water extracts was only observed for Listeria monocytogenes (93.8-375.0 microg/mL) and Staphylococcus epidermidis (354.2 microg/mL). The minimum concentration required to inhibit Zygosaccharomyces bailii was 500 microg/mL for the ethanol extracts, while no inhibition was observed for the water extracts. No inhibition by either ethanol or water extracts was observed against Penicillium spp. and Aspergillus flavus.

Comparison of next generation sequencing technologies for transcriptome characterization

Background

We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG) ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis.

Results

The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB), 119,518 (88.7%) mapped exactly to known exons, while 1,117 (0.8%) mapped to introns, 11,524 (8.6%) spanned annotated intron/exon boundaries, and 3,066 (2.3%) extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics.

Conclusion

NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance over capillary-based sequencing, but NG sequencing also presents significant challenges in assembly and sequence accuracy due to short read lengths, method-specific sequencing errors, and the absence of physical clones. These problems may be overcome by hybrid sequencing strategies using a mixture of sequencing methodologies, by new assemblers, and by sequencing more deeply. Sequencing and microarray outcomes from multiple experiments suggest that our simulator will be useful for guiding NG transcriptome sequencing projects in a wide range of organisms.

Floral variation and floral genetics in basal angiosperms

Recent advances in phylogeny reconstruction and floral genetics set the stage for new investigations of the origin and diversification of the flower. We review the current state of angiosperm phylogeny, with an emphasis on basal lineages. With the surprising inclusion of Hydatellaceae with Nymphaeales, recent studies support the topology of Amborella sister to all other extant angiosperms, with Nymphaeales and then Austrobaileyales as subsequent sisters to all remaining angiosperms. Notable modifications from most recent analyses are the sister relationships of Chloranthaceae with the magnoliids and of Ceratophyllaceae with eudicots. We review "trends" in floral morphology and contrast historical, intuitive interpretations with explicit character-state reconstructions using molecular-based trees, focusing on (1) the size, number, and organization of floral organs; (2) the evolution of the perianth; (3) floral symmetry; and (4) floral synorganization. We provide summaries of those genes known to affect floral features that contribute to much of floral diversity. Although most floral genes have not been investigated outside of a few model systems, sufficient information is emerging to identify candidate genes for testing specific hypotheses in nonmodel plants. We conclude with a set of evo-devo case studies in which floral genetics have been linked to variation in floral morphology.