Genomic and transcriptomic inventory of membrane transporters in coffee: Exploring molecular mechanisms of metabolite accumulation

The genus Coffea (Rubiaceae) encompasses a group of perennial plant species, including a commodity crop from which seeds are roasted, ground, and infused to make one of the most appreciated beverages in the world. As an important tropical crop restricted to specific regions of the world, coffee production is highly susceptible to the effects of environmental instabilities (i.e., local year-to-year weather fluctuations and global climate change) and threatening pest pressures, not to mention an increasing quality rigor by consumers in industrialized countries. Specialized metabolites are substances that largely affect plant-environment interactions as well as how consumers experience agricultural products. Membrane transporters are key targets, albeit understudied, for understanding and tailoring the spatiotemporal distribution of specialized metabolites as they mediate and control molecular trafficking and substance accumulation. Therefore, we analyzed the transportome of C. canephora encoded within the 25,574 protein-coding genes annotated in the genome of this species and identified 1847 putative membrane transporters. Following, we mined 152 transcriptional profiles of C. canephora and C. arabica and performed a comprehensive co-expression analysis to identify transporters potentially involved in the accumulation of specialized metabolites associated with beverage quality and bioactivity attributes. In toto, this report points to an avenue of possibilities on Coffea genomic and transcriptomic data mining for genetic breeding strategies, which can lead to the development of new, resilient varieties for more sustainable coffee production systems.

Gene Expression Profile Analysis is Directly Affected by the Selected Reference Gene: The Case of Leaf-Cutting Atta Sexdens

Although several ant species are important targets for the development of molecular control strategies, only a few studies focus on identifying and validating reference genes for quantitative reverse transcription polymerase chain reaction (RT-qPCR) data normalization. We provide here an extensive study to identify and validate suitable reference genes for gene expression analysis in the ant Atta sexdens, a threatening agricultural pest in South America. The optimal number of reference genes varies according to each sample and the result generated by RefFinder differed about which is the most suitable reference gene. Results suggest that the RPS16, NADH and SDHB genes were the best reference genes in the sample pool according to stability values. The SNF7 gene expression pattern was stable in all evaluated sample set. In contrast, when using less stable reference genes for normalization a large variability in SNF7 gene expression was recorded. There is no universal reference gene suitable for all conditions under analysis, since these genes can also participate in different cellular functions, thus requiring a systematic validation of possible reference genes for each specific condition. The choice of reference genes on SNF7 gene normalization confirmed that unstable reference genes might drastically change the expression profile analysis of target candidate genes.

Histodifferentiation of oil palm somatic embryo development at low auxin concentration

Large-scale propagation of oil palm (Elaeis guineensis, Jacq.) is difficult due to its single apical meristem. Thus, obtaining plants is mainly through seed germination, and a long growing period is required before oil production is possible. An alternative to large-scale seedling production is indirect somatic embryogenesis. The aim of this study was to analyze the somatic embryogenesis process in oil palm (E. guineensis Jacq.) with amino acids and low concentrations of auxins. The Tenera hybrid was analyzed by cytochemical and ultrastructural methods and was used to regenerate oil palm plants. First, calli were induced in MS culture media supplemented with 2,4-D and picloram. Two types of calli were obtained, characterized by beige or translucent color. Beige calli had embryogenic characteristics, such as large nuclei with prominent nucleoli, and they were multiplied for 8 months in MM culture (half strength MS, 1 mg L^-1 2,4-D, 2 mg L^-1 2iP, 1 mg L^-1 IBA, 250 mg L^-1 citric acid, 10 mg L^-1 cysteine, 100 mg L^-1 inositol, 1 mg L^-1 thiamine, 1 mg L^-1 pyridoxine, 1 mg L^-1 nicotinic acid, 1 mg L^-1 glycine, 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate). After multiplication, the MCB culture medium (half strength MS, supplemented with 0.25 mg L^-1 NAA, 2 mg L^-1 BAP, MM vitamins and 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate) was the most efficient for embryo formation, showing meristematic centers with totipotent cells in histochemical analyses. The somatic embryos were developed and germinated in MG medium (half strength MS, 0.45 mg L^-1 IAA, 0.25 mg L^-1 BAP, and MM vitamins), transplanted into polyethylene tubes containing pine bark substrates, and acclimatized in a greenhouse, achieving a 97% survival rate. The use of picloram for callus induction and somatic embryogenesis is advantageous and multiplication in MM medium is an important step for increasing cell mass. The calli with light beige color and nodular structures have meristematic cells with dense cytoplasm and totipotential features that later give rise to protoderm, procambium, and ground meristem during the globular, cordiform, and torpedo embryogenesis phases. In MCB medium, the concentration of vitamins and amino acids are crucial for somatic embryogenesis.

Molecular epidemiology of Streptococcus agalactiae isolated from mastitis in Brazilian dairy herds

Streptococcus agalactiae is one of the most common pathogens leading to mastitis in dairy herds worldwide; consequently, the pathogen causes major economic losses for affected farmers. In this study, multilocus sequence typing (MLST), genotypic capsular typing by multiplex polymerase chain reaction (PCR), and virulence gene detection were performed to address the molecular epidemiology of 59 bovine (mastitis) S. agalactiae isolates from 36 dairy farms located in the largest milk-producing mesoregions in Brazil (Minas Gerais, São Paulo, Paraná, and Pernambuco). We screened for the virulence genes bac, bca, bibA, cfb, hylB, fbsA, fbsB, PI-1, PI-2a, and PI-2b, which are associated with adhesion, invasion, tissue damage, and/or immune evasion. Furthermore, five capsular types were identified (Ia, Ib, II, III, and IV), and a few isolates were classified as non-typeable (NT). MLST revealed the following eight sequence types (STs): ST-61, ST-67, ST-103, ST-146, ST-226, ST-314, and ST-570, which were clustered in five clonal complexes (CC64, CC67, CC103, CC17, and CC314), and one singleton, ST-91. Among the virulence genes screened in this study, PI-2b, fbsB, cfb, and hylB appear to be the most important during mastitis development in cattle. Collectively, these results establish the molecular epidemiology of S. agalactiae isolated from cows in Brazilian herds. We believe that the data presented here provide a foundation for future research aimed at developing and implementing new preventative and treatment options for mastitis caused by S. agalactiae.

Subspecies and diet affect the expression of genes involved in lipid metabolism and chemical composition of muscle in beef cattle

Fourteen Nellore and 14 Angus young bulls with BW of 381±11.8kg were randomly assigned into 2 feeding groups (whole shelled corn without forage (WSC) or corn silage and ground corn (GC)) to evaluate chemical composition and expression of genes involved in lipid metabolism in the longissimus thoracis (LT). We hypothesized that bulls fed the WSC diet have greater amounts of intramuscular fat and Angus have higher expression levels of PPAR and SREBF. Meat from Angus bulls had greater ether extract compared to Nellore (P<0.05). Muscle from bulls fed the WSC diet had greater expression of PPARA (P<0.05) and lower levels of SREBF1 expression (P<0.01). The LT of Nellore fed GC had greater expression of FABP4, ACACA and SCD genes (P<0.01). In conclusion, the greater concentration of starch in the WSC diet did not increase marbling in the beef of bulls fed this diet due to the reduced expression of SREBF1.

Expression of genes related to the regulation of muscle protein turnover in Angus and Nellore bulls

We aimed to evaluate the expression of genes related to the regulation of muscle protein turnover in the longissimus dorsi (LD) muscle of Angus and Nellore bulls and to estimate the within-breed correlations of gene expression and performance traits. Thirteen genes related to the IGF-1 and myostatin pathways were studied. Thirteen animals, with an initial average BW of 381.2 ± 11.8 kg, from each breed were used in a completely randomized 2 × 2 factorial design (2 breeds and 2 feeding levels). The diet consisted of corn silage and a corn-soybean meal concentrate in a roughage-to-concentrate ratio of 30:70. Cattle were fed ad libitum (with 9 animals from each breed) or feed restricted (a 55% restriction of total DMI of ad libitum-fed animals, calculated as percentage of metabolic BW, with 4 animals of each breed). The experimental period lasted for 82 d and it was preceded by a 28-d adaptation period. The performance traits evaluated were slaughter body weight, total ADG (from d 1 to 82 of the trial), initial ADG (from d 1 to 41 of the trial), final ADG (from d 42 to 82 of the trial), total DMI (from d 1 to 82 of the trial), initial DMI (from d 1 to 41 of the trial), final DMI (from d 42 to 82 of the trial), HCW, LD weight (LDW), and rib eye area (REA). After slaughter, samples were taken from the LD muscle between the 12th and 13th ribs for gene expression analysis by quantitative reverse transcription PCR. There was no difference ( > 0.05) in the expression of any of the genes studied between ad libitum-fed Angus and ad libitum-fed Nellore, whereas feed restriction increased the expression of (; < 0.001), (; = 0.05), and (; = 0.04) and decreased the expression of ( < 0.01). The REA was negatively correlated to (; = 0.01), (; = 0.02), and ( = 0.05). The HCW was negatively correlated to ( = 0.01) and ( = 0.01) and tended to be negatively correlated to ( = 0.07), whereas the LDW tended to be negatively correlated to ( = 0.08). The genes , , and seem to be important for muscle growth and may be worthy of further investigation as future strategies for increasing muscle in livestock.

The proteome profile of embryogenic cell suspensions of Coffea arabica L

Somatic embryogenesis, is a process by which new viable embryos are produced from somatic tissues. Somatic embryogenesis is not only a useful biotechnological tool for the massive clonal propagation and genetic engineering but it also allows to obtain fundamental knowledge about the molecular changes that take place during embryogenesis. We present the proteome profile of two embryogenic cell suspensions. We identified 1052 non-redundant proteins. We present their known GO annotations and show two protein networks sharing the GO annotations related to stress and embryogenic capacity via the free program Cytoscape. To our knowledge these results give the first high-throughput proteome description of embryogenic cell suspensions and provide new information about somatic embryos for the whole plant community. The published proteome is a first step toward understanding somatic embryogenesis in coffee and toward a better annotation of proteins in an important non-model crop. All data are available via ProteomeXchange with identifier PXD002963.

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

Expression of genes involved in lipid metabolism in the muscle of beef cattle fed soybean or rumen-protected fat, with or without monensin supplementation

Degree of unsaturation of fatty acids, which is influenced by lipid source and level of metabolism in the rumen, is a major determinant in how dietary lipids affect genes that regulate beef marbling. A total of 28 Red Norte bulls with an initial live weight of 361±32 kg (P>0.05) were used in a completely randomized experimental design to analyze the expression of genes that are involved in lipid metabolism in the longissimus dorsi (LD) when diets contained soybean grain or rumen-protected fat, with or without monensin. Treatments were arranged as a 2×2 factorial, with 4 treatments and 7 replicates per treatment. Half of the animals that received soybean or rumen-protected fat were supplemented with 230 mg head(-1) d(-1) of monensin. Gene expression was analyzed by reverse-transcription quantitative PCR (RT-qPCR). Expression of sterol regulatory element-binding protein-1c (SREBP-1c) in the LD muscle was not affected by lipid source or monensin (P>0.05). There was an interaction effect (P<0.05) between lipid source and monensin for peroxisome proliferator-activated receptor α (PPAR-α) and stearoyl-CoA desaturase (SCD) expression, where greater gene expression was found in animals fed soybean plus monensin and the lower gene expression was found in animals fed rumen-protected fat plus monensin. Expression of lipoprotein lipase (LPL) and fatty acid-binding protein 4 (FABP4) were greater (P<0.05) in the LD muscle of animals fed soybean. Monensin had no effect on LPL and FABP4 expression when soybean without monensin was fed, but when rumen-protected fat was fed, monensin increased LPL expression and decreased FABP4 expression (P<0.05). Linoleic and arachidonic acids had negative correlations (P<0.05) with the expression of PPAR-α, SCD, FABP4, and LPL genes. PPAR-α gene expression was not correlated with SREBP-1c but was positively correlated with SCD, FABP4, LPL, and glutathione peroxidase (GPX1) gene expression (P<0.001). Lipid sources and monensin interact and alter the expression of PPAR-α, SCD, acetyl CoA carboxylase α (ACACA), LPL, FABP4, and GPX1. These changes in gene expression were most associated with arachidonic and α-linolenic acids and the ability of lipid sources and monensin to increase these fatty acids in tissues.

Identification and expression analysis of ethylene biosynthesis and signaling genes provides insights into the early and late coffee cultivars ripening pathway

The plant hormone ethylene is involved in the regulation of a multitude of plant processes, ranging from seed germination to organ senescence. Ethylene induces fruit ripening in climacteric fruits, such as coffee, being directly involved in fruit ripening time and synchronization. Coffee early cultivars usually show a more uniform ripening process although little is known about the genetic factors that promote the earliness of ripening. Thus, this work aimed to characterize the putative members of the coffee (Coffea arabica) ethylene biosynthesis and signaling pathways, as well as to analyze the expression patterns of these members during fruit ripening of early (Catucaí 785-15) and late (Acauã) coffee cultivars. Reverse Transcription-qPCR analysis of the four biosynthesis genes (CaACS1-like; CaACO1-like; CaACO4-like e CaACO5-like) analyzed in this study showed that CaACO1-like and CaACO4-like displayed an expression pattern typically observed in climacteric fruits, being up-regulated during ripening. CaACS1-like gene expression was also up-regulated during fruit ripening of both cultivars, although in a much lesser extent when compared to the changes in CaACO1-like and CaACO4-like gene expression. CaACO5-like was only induced in raisin fruit and may be related to senescence processes. On the other hand, members of the ethylene signaling pathway (CaETR1-like, CaETR4-like, CaCTR2-like, CaEIN2-like, CaEIN3-like, CaERF1) showed slightly higher expression levels during the initial stages of development (green and yellow-green fruits), except for the ethylene receptors CaETR1-like and CaETR4-like, which were constitutively expressed and induced in cherry fruits, respectively. The higher ethylene production levels in Catucaí 785-15 fruits, indicated by the expression analysis of CaACO1-like and CaACO4-like, suggest that it promotes an enhanced CaETR4-like degradation, leading to an increase in ethylene sensitivity and consequently to an earliness in the ripening process of this cultivar. Ethylene production in Acauã fruits may not be sufficient to inactivate the CaETR4-like levels and thus ripening changes occur in a slower pace. Thus, the expression analysis of the ethylene biosynthesis and signaling genes suggests that ethylene is directly involved in the determination of the ripening time of coffee fruits, and CaACO1-like, CaACO4-like and CaETR4-like may display essential roles during coffee fruit ripening.

Identification of expressed sequences in the coffee genome potentially associated with somatic embryogenesis

Brazil possesses the most modern and productive coffee growing farms in the world, but technological development is desired to cope with the increasing world demand. One way to increase Brazilian coffee growing productivity is wide scale production of clones with superior genotypes, which can be obtained with in vitro propagation technique, or from tissue culture. These procedures can generate thousands of clones. However, the methodologies for in vitro cultivation are genotype-dependent, which leads to an almost empirical development of specific protocols for each species. Therefore, molecular markers linked to the biochemical events of somatic embryogenesis would greatly facilitate the development of such protocols. In this context, sequences potentially involved in embryogenesis processes in the coffee plant were identified in silico from libraries generated by the Brazilian Coffee Genome Project. Through these in silico analyses, we identified 15 EST-contigs related to the embryogenesis process. Among these, 5 EST-contigs (3605, 9850, 13686, 17240, and 17265) could readily be associated with plant embryogenesis. Sequence analysis of EST-contig 3605, 9850, and 17265 revealed similarity to a polygalacturonase, to a cysteine-proteinase, and to an allergenine, respectively. Results also show that EST-contig 17265 sequences presented similarity to an expansin. Finally, analysis of EST-contig 17240 revealed similarity to a protein of unknown function, but it grouped in the similarity dendrogram with the WUSCHEL transcription factor. The data suggest that these EST-contigs are related to the embryogenic process and have potential as molecular markers to increase methodological efficiency in obtaining coffee plant embryogenic materials.

Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains

Background

Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.

Methodology and Findings

We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer.

Conclusions

These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.