Cross-species Studies Research Articles

Expression and prognostic significance of vascular endothelial growth factor-A (VEGF-A) and its receptor in canine prostate cancer.

Vascular endothelial growth factor-A (VEGF-A) and its receptor, VEGF receptor-2 (VEGFR-2), represent a complex family of angiogenic molecules consisting of different ligands and receptors. Due to the importance of VEGF-A/VEGFR-2 signaling in tumor proliferation and angiogenesis, this study aimed to evaluate the protein and gene expression levels of VEGF-A and VEGFR-2 in canine prostate cancer (PC). We analyzed VEGF-A and VEGFR-2 expression in 87 PC samples by immunohistochemistry and quantitative-polymerase chain reaction. PC samples were graded according to the Gleason score and the immunohistochemical staining for VEGF-A and VEGFR-2 was quantified using a selected threshold from the ImageJ Software. Microvascular density was assessed by cluster of differentiation 31 staining and counting the number of positive vessels. Additionally, the homology of VEGF-A and VEGFR-2 between humans and dogs was assessed, followed by the construction of a protein structure homology model to compare the tertiary structures of these proteins in both species. Negative to weakly positive expression levels of VEGF-A and VEGFR-2 were observed in the epithelial cells of the normal prostate (NP) and prostatic hyperplasia samples. In contrast, the canine proliferative atrophy and PC samples exhibited higher VEGF-A (p < .0001) and VEGFR-2 (p < .0001) compared to NP. Moreover, positive correlations between the expression levels of VEGF-A and VEGFR-2 (Spearman's coefficient (r) = .68, p = .013) and the expression levels of VEGF-A and VEGFR-2 proteins (r = .8, p < .0001) were also observed in the NP samples. Additionally, the patients with PC exhibiting higher VEGFR-2 expression levels experienced a shorter survival period (p = .0372). Furthermore, we found an association between the microvascular density and overall survival. Dogs with a higher number of vessels showed a shorter survival time. We further demonstrated that the VEGF-A and VEGFR-2 exhibited high homology between humans and dogs, and identified their protein structures in both species. In conclusion, VEGFR-2 appears to be an independent prognostic factor in animals with PC. VEGF-A and VEGFR-2 are highly conserved between humans and dogs, which can be investigated further in future cross-species studies to explore their therapeutic applications.

Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging.

Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels.

Identification and validation of in silico mined polymorphic EST-SSR for genetic diversity and cross-species transferability studies in Safflower

Identification and validation of in silico mined polymorphic EST-SSR for genetic diversity and cross-species transferability studies in Safflower

Regulatory and Coding Sequences of TRNP1 Co-Evolve With Cortical Folding in Mammals

Genomes can be seen as notebooks of evolution on successful genetic experiments. Comparing genomes across species allows identifying conserved DNA regions responsible for conserved biological functions, but additional information could be leveraged when also considering phenotypic variance across species. Here, we exemplify such a association study for the gene TRNP1 that is known to be important for brain growth and cortical folding in mice and ferrets.We find that the rate of TRNP1 protein evolution (ω) co-evolves with the rate of cortical folding across mammals and that TRNP1 proteins from species with more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay (MPRA) and identify one CRE that also co-evolves with cortical folding in Old World Monkeys and Apes. Our analyses indicate that coding and regulatory changes in TRNP1 have modulated its activity to adjust cortical folding during mammalian evolution. They also provide a blueprint how cross-species association studies could help to better understand the evolution and the molecular mechanisms of phenotypes.

Cross-species studies on orbitofrontal control of inference-based behavior.

Many decisions are guided by expectations about their outcomes. These expectations can arise from two fundamentally different sources: from direct experience with outcomes and the events and actions that precede them or from mental simulations and inferences when direct experience is missing. Here we discuss four elegant tasks from animal learning theory (devaluation, sensory preconditioning, Pavlovian-to-instrumental transfer, and Pavlovian overexpectation) and how they can be used to isolate behavior that is based on such mental simulations from behavior that can be based solely on experience. We then review findings from studies in rodents, nonhuman primates, and humans that use these tasks in combination with neural recording and loss-of-function experiments to understand the role of the orbitofrontal cortex (OFC) in outcome inference. The results of these studies show that activity in the OFC is correlated with inferred outcome expectations and that an intact OFC is necessary for inference-based behavior and learning. In summary, these findings provide converging cross-species support for the idea that the OFC is critical for behavior that is based on inferred outcomes, whereas it is not required when expectations can be based on direct experience alone. This conclusion may have important implications for our understanding of the role of OFC in psychiatric disorders and how we may be able to treat them. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Chronic Low Dose Neutron Exposure Results in Altered Neurotransmission Properties of the Hippocampus-Prefrontal Cortex Axis in Both Mice and Rats.

The proposed deep space exploration to the moon and later to Mars will result in astronauts receiving significant chronic exposures to space radiation (SR). SR exposure results in multiple neurocognitive impairments. Recently, our cross-species (mouse/rat) studies reported impaired associative memory formation in both species following a chronic 6-month low dose exposure to a mixed field of neutrons (1 mGy/day for a total dose pf 18 cGy). In the present study, we report neutron exposure induced synaptic plasticity in the medial prefrontal cortex, accompanied by microglial activation and significant synaptic loss in the hippocampus. In a parallel study, neutron exposure was also found to alter fluorescence assisted single synaptosome LTP (FASS-LTP) in the hippocampus of rats, that may be related to a reduced ability to insert AMPAR into the post-synaptic membrane, which may arise from increased phosphorylation of the serine 845 residue of the GluA1 subunit. Thus, we demonstrate for the first time, that low dose chronic neutron irradiation impacts homeostatic synaptic plasticity in the hippocampal-cortical circuit in two rodent species, and that the ability to successfully encode associative recognition memory is a dynamic, multicircuit process, possibly involving compensatory changes in AMPAR density on the synaptic surface.

A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen

Pseudomonas aeruginosa is an important opportunistic human pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now, P. aeruginosa proteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under different conditions and from diverse cellular compartments have been joined to build the Pseudomonas PeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome of P. aeruginosa PAO1, the highest coverage among bacterial PeptideAtlas datasets. The proteins included cover 89% of metabolic proteins, 72% of proteins involved in genetic information processing, 83% of proteins responsible for environmental information processing, more than 88% of the ones related to quorum sensing and biofilm formation, and 89% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. The manuscript describes the building of the PeptideAtlas and the contribution of the different proteomic data used. SignificancePseudomonas aeruginosa is among the most versatile human bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.

Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.

First set of microsatellite markers for immortelle (Helichrysum italicum (Roth) G. Don): A step towards the selection of the most promising genotypes for cultivation

Immortelle (Helichrysum italicum (Roth) G. Don), also known as curry plant, is a herbaceous perennial plant with documented biological properties that contribute to its attractiveness and use in the cosmetic, pharmaceutical, and food industry. Availability of DNA markers can significantly improve the knowledge of complex genetics and biochemistry of this aromatic plant. To improve in-depth genetic studies, high-throughput sequencing of a genomic DNA has been performed and a set of 24 SSR markers was developed. In total, 17,025,076 high quality reads were assembled in contigs with the cumulative length of 258.6 Mbp. Genome-wide microsatellite sequences were identified in 8.19% (36,882) contigs, among which dinucleotide (71.2%) and trinucleotide (24.4%) repeats were the most abundant. Twenty-four finally selected microsatellite loci (including di- and tri-nucleotides) which exhibited polymorphism with unambiguous and reproducible amplification products, were used for detailed genetic diversity analysis on a set of 28 H. italicum samples. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method based on the Jaccard index differentiated 27 genotypes into two main clusters according to their geographical origin (Northern and Southern Adriatic region), whereas the commercially available plant did not cluster with other H. italicum individuals and morphological evaluation confirmed that it belongs to Helichrysum angustifolium (Lam.) DC. The great diversity of H. italicum samples from the Adriatic observed by new microsatellites will serve for selection of most promising genotypes for propagation and their implementation in agricultural production. The first set of microsatellites developed in the present study provides a valuable resource of DNA markers for further breeding programs, germplasm characterization, and cross-species transferability studies.

Complementary and Integrated Studies of Longevity and Healthy Aging

Five NIH-funded studies, the Long Life Family Study (LLFS, U19), the Longevity Consortium (LC, U19), Longevity Genomics (U24), and Protective Omics Profiles in Centenarians (UH2) work together to triangulate on mechanisms of extreme longevity and healthy aging with the ultimate goal of discovering predictors and targetable pathways. Linkage analyses by LLFS identified extremely strong genetic linkage peaks for cross-sectional as well as longitudinal trajectory rates-of-change phenotypes. Deep sequencing suggests these peaks are driven by rare, protective variants in selected pedigrees. In cross-species studies (UH2, LC), genomics, metabolomics and proteomics are used to exploit many-fold variances in natural life spans to discover protective mechanisms that explain some of these differences. Proteome analysis reveal several longevity-related proteins such as Cip1/p21, FOXO3, TOP2A, AKT1, RICTOR, INSR and SIRT6 harboring post translational modification sites that preferentially appear in short- versus long-lived species. The U24 effort developed a tool using genetically-mediated gene expression to prioritize genes for longevity translational efforts. We found that BLOC1S1 was associated with longevity and protection from atrial fibrillation and hearing loss without being associated with adverse events. This novel target is undergoing functional characterization. A proteomic assay (4,131 proteins, Somascan) annotated by genome-wide association study results in a total of 1,797 centenarians and 3,685 controls divided into independent discovery and replication sets, discovered significant and replicated over-expression (thus, pro-longevity) of BIRC2 and under-expression of APOB in carriers of the APOE ɛ-2 allele. A novel protein signature of rs2184061 (CDKN2a/CDKN2B in chromosome 9) was also associated with slower aging.

Both HIV and Tat expression decrease prepulse inhibition with further impairment by methamphetamine

HIV infection and methamphetamine (METH) use are highly comorbid and represent a significant public health problem. Both conditions are known to negatively impact a variety of brain functions. One brain function that may be affected by HIV and METH use is sensorimotor gating, an automatic, pre-conscious filtering of sensory information that is thought to contribute to higher order cognitive processes. Sensorimotor gating is often measured using prepulse inhibition (PPI), a paradigm that can be conducted in both humans and animals, thereby enabling cross-species translational studies. While previous studies suggest HIV and METH may individually impair PPI, little research has been conducted on the effects of combined HIV and METH on PPI. The goal of this cross-species study was to determine the effects of METH on PPI in the inducible Tat (iTat) mouse model of HIV and in people with HIV. PPI was measured in the iTat mouse model before, during, and after chronic METH treatment and after Tat induction. Chronic METH treatment decreased PPI in male but not female mice. PPI normalized with cessation of METH. Inducing Tat expression decreased PPI in male but not in female mice. No interactions between chronic METH treatment and Tat expression were observed in mice. In humans, HIV was associated with decreased PPI in both men and women. Furthermore, PPI was lowest in people with HIV who also had a history of METH dependence. Overall, these results suggest HIV and METH may additively impair early information processing in humans, potentially affecting downstream cognitive function.

Survey of canine use and safety of isoxazoline parasiticides.

A veterinarian and pet owner survey (Project Jake) examined the use and safety of isoxazoline parasiticides given to dogs. Data were received during August 1–31, 2018 from a total of 2,751 survey responses. Forty‐two percent (1,157) reported no flea treatment or adverse events (AE), while 58% (1594) had been treated with some parasiticide for flea control, and of those that received a parasiticide, the majority, or 83% (1,325), received an isooxazoline. When any flea treatment was given, AE were reported for 66.6% of respondents, with no apparent AE noted for 36.1%. Project Jake findings were compared to a retrospective analysis of publicly available Food and Drug Administration (FDA) and European Medicines Agency (EMA) reported AE. The number of total AE reported to FDA and EMA were comparable, although a 7 to 10 times higher occurrence of death and seizures was reported from the EMA or from outside the United States (US). Serious AE responses for death, seizures and neurological effects reported in our survey were higher than the FDA but moderately lower than the EMA reports. These sizable global data sets combined with this pre‐ and post‐parasiticide administration survey indicated that isoxazoline neurotoxicity was not flea‐ and tick‐specific. Post‐marketing serious AE were much higher than in Investigational New Drug (IND) submissions. Although the labels have recently been updated, dogs, cats and their caregivers remain impacted by their use. These aggregate data reports support the need for continued cross‐species studies and critical review of product labelling by regulatory agencies and manufacturers.

Replication of Influenza D Viruses of Bovine and Swine Origin in Ovine Respiratory Explants and Their Attachment to the Respiratory Tract of Bovine, Sheep, Goat, Horse, and Swine.

Bovine is considered the main reservoir of influenza D virus (IDV), however, low levels of seropositivity in other farmed species suggest a wide range of potential hosts. Nevertheless, it is not clear whether this scenario is the result of rare spillover events upon contact with bovines, or a lack of adaptation of IDV to these hosts. Among these species, sheep represents a crucial component of the rural economy in many developing countries, but little is known about its role in the ecology of the disease. To evaluate the susceptibility of sheep to IDV viruses of different origin, we used ovine respiratory tissues as an ex vivo model and investigated the infective phenotype of two IDV strains isolated from either bovine (IDV-BOV) or swine (IDV-SW). For translatability purposes, we included a parainfluenza type 3 virus, as positive control, given its known respiratory tropism in sheep. We performed a timed evaluation of the viral infectivity, cell tropism and the associated histopathology, by means of tissue culture infectious dose assays on supernatants and histological/immunohistochemical analyses on explanted tissues, respectively. To further investigate differences in the phenotype of these two strains and to identify the potential targets of replication in the most commonly land-based farmed mammalian species, we carried out virus binding assays on histological sections of the respiratory tract of bovine, caprine, ovine, horse and swine. Our results demonstrated that IDV successfully replicates in nasal, tracheal and lung ovine tissues, suggesting a moderate susceptibility of this species to IDV infection. Interestingly, despite the high genetic identity of these strains, IDV- BOV consistently replicated to higher titers than IDV-SW in all respiratory tracts, suggesting IDV viruses might display considerable levels of variability in their phenotype when crossing the species barrier. Virus binding assays confirmed a superior affinity of the IDV viruses for the bovine upper respiratory tract, and a preference for the pharyngeal epithelium of small ruminants, indicating possible targets to improve the sensitivity of virological sampling for diagnostic and post-mortem purposes. Further pathogenesis and cross-species transmission studies will be necessary to elucidate the ecology of IDV and eventually allow the design of cost-effective surveillance strategies.

FERM domain\u2013containing protein 6 identifies a subpopulation of varicose nerve fibers in different vertebrate species

FERM domain–containing protein 6 (FRMD6) is a member of the FERM protein superfamily, which is evolutionary highly conserved and has recently been identified as an upstream regulator of the conserved growth-promoting Hippo signaling pathway. In clinical studies, the FRMD6 gene is correlated with high significance to Alzheimer’s disease and cognitive impairment implicating a wider role of this protein in the nervous system. Scare data are available on the localization of endogenous FRMD6 in neural tissues. Using a FRMD6-directed antiserum, we detected specific immunoreactivity in varicose nerve fibers in the rat central and peripheral nervous system. FRMD6-immunoreactive (-ir) neurons were found in the sensory ganglia of cranial nerves, which were marked by a pool of labeled cytoplasmic granules. Cross-species comparative studies detected a morphologically identical fiber population and a comparable fiber distribution in tissues from xenopus and human cranial nerves and ganglia. In the spinal cord, FRMD6-ir was detectable in the terminal endings of primary afferent neurons containing substance P (SP). In the rat diencephalon, FRMD6-ir was co-localized with either SP- or arginine vasopressin–positive fibers in Broca’s diagonal band and the lateral septum. Dense fiber terminals containing both FRMD6-ir and growth hormone-releasing hormone were found in the median eminence. The intimate association of FRMD6 with secretory vesicles was investigated in vitro. Induction of exocytotic vesicles in cultured cells by ectopic expression of the SP precursor molecule preprotachykinin A led to a redistribution and co-localization of endogenous FRMD6 with secretory granules closely mimicking the observations in tissues.

The Evolution of Functional Traits in Plants: Is the Giant Still Sleeping?

The Evolution of Functional Traits in Plants: Is the Giant Still Sleeping?

Economic Decisions through Circuit Inhibition.

Economic choices between goods are thought to rely on the orbitofrontal cortex (OFC), but the decision mechanisms remain poorly understood. To shed light on this fundamental issue, we recorded from the OFC of monkeys choosing between two juices offered sequentially. An analysis of firing rates across time windows revealed the presence of different groups of neurons similar to those previously identified under simultaneous offers. This observation suggested that economic decisions in the two modalities are formed in the same neural circuit. We then examined several hypotheses on the decision mechanisms. OFC neurons encoded good identities and values in a juice-based representation (labeled lines). Contrary to previous assessments, our data argued against the idea that decisions rely on mutual inhibition at the level of offer values. In fact, we showed that previous arguments for mutual inhibition were confounded by differences in value ranges. Instead, decisions seemed to involve mechanisms of circuit inhibition, whereby each offer value indirectly inhibited neurons encoding the opposite choice outcome. Our results reconcile a variety of previous findings and provide a general account for the neuronal underpinnings of economic choices.

Ancestral reconstruction of protein interaction networks.

The molecular and cellular basis of novelty is an active area of research in evolutionary biology. Until very recently, the vast majority of cellular phenomena were so difficult to sample that cross-species studies of biochemistry were rare and comparative analysis at the level of biochemical systems was almost impossible. Recent advances in systems biology are changing what is possible, however, and comparative phylogenetic methods that can handle this new data are wanted. Here, we introduce the term “phylogenetic latent variable models” (PLVMs, pronounced “plums”) for a class of models that has recently been used to infer the evolution of cellular states from systems-level molecular data, and develop a new parameterization and fitting strategy that is useful for comparative inference of biochemical networks. We deploy this new framework to infer the ancestral states and evolutionary dynamics of protein-interaction networks by analyzing >16,000 predominantly metazoan co-fractionation and affinity-purification mass spectrometry experiments. Based on these data, we estimate ancestral interactions across unikonts, broadly recovering protein complexes involved in translation, transcription, proteostasis, transport, and membrane trafficking. Using these results, we predict an ancient core of the Commander complex made up of CCDC22, CCDC93, C16orf62, and DSCR3, with more recent additions of COMMD-containing proteins in tetrapods. We also use simulations to develop model fitting strategies and discuss future model developments.

Synthesis and Preliminary Evaluation of [11 C]GNE-1023 as a Potent PET Probe for Imaging Leucine-Rich Repeat Kinase 2 (LRRK2) in Parkinson's Disease.

Leucine-rich repeat kinase 2 (LRRK2) is a large protein involved in the pathogenesis of Parkinson's disease (PD). It has been demonstrated that PD is mainly conferred by LRRK2 mutations that bring about increased kinase activity. As a consequence, selective inhibition of LRRK2 may help to recover the normal functions of LRRK2, thereby serving as a promising alternative therapeutic target for PD treatment. The mapping of LRRK2 by positron emission tomography (PET) studies allows a thorough understanding of PD and other LRRK2-related disorders; it also helps to validate and translate novel LRRK2 inhibitors. However, no LRRK2 PET probes have yet been reported in the primary literature. Herein we present a facile synthesis and preliminary evaluation of [11 C]GNE-1023 as a novel potent PET probe for LRRK2 imaging in PD. [11 C]GNE-1023 was synthesized in good radiochemical yield (10 % non-decay-corrected RCY), excellent radiochemical purity (>99 %), and high molar activity (>37 GBq μmol-1 ). Excellent in vitro binding specificity of [11 C]GNE-1023 toward LRRK2 was demonstrated in cross-species studies, including rat and nonhuman primate brain tissues by autoradiography experiments. Subsequent whole-body biodistribution studies indicated limited brain uptake and urinary and hepatobiliary elimination of this radioligand. This study may pave the way for further development of a new generation of LRRK2 PET probes.

Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei.

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

Fruit Salad in the Lab: Comparing Botanical Species to Help Deciphering Fruit Primary Metabolism.

Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration of fruit development, coordination of ripening changes (climacteric vs. non-climacteric type) and biochemical composition at ripeness is linked to sweetness and acidity. The main constituents of mature fruit result from different strategies of carbon transport and metabolism. Thus, the timing and nature of phloem loading and unloading can largely differ from one species to another. Furthermore, accumulations and transformations of major soluble sugars, organic acids, amino acids, starch and cell walls are very variable among fruit species. Comparing fruit species therefore appears as a valuable way to get a better understanding of metabolism. On the one hand, the comparison of results of studies about species of different botanical families allows pointing the drivers of sugar or organic acid accumulation but this kind of comparison is often hampered by heterogeneous analysis approaches applied in each study and incomplete dataset. On the other hand, cross-species studies remain rare but have brought new insights into key aspects of primary metabolism regulation. In addition, new tools for multi-species comparisons are currently emerging, including meta-analyses or re-use of shared metabolic or genomic data, and comparative metabolic flux or process-based modeling. All these approaches contribute to the identification of the metabolic factors that influence fruit growth and quality, in order to adjust their levels with breeding or cultural practices, with respect to improving fruit traits.