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Proceedings of the National Academy of... Nov 2021Strawberry ( spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been... (Comparative Study)
Comparative Study
Strawberry ( spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species ( Jia J. Lei). Finally, we constructed a pan-genome for and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.
Topics: Biological Evolution; Fragaria; Genetic Variation; Genome, Plant; Phylogeography; Pigmentation; Selection, Genetic; Whole Genome Sequencing
PubMed: 34697247
DOI: 10.1073/pnas.2105431118 -
ELife Jan 2022In the common sunflower, patterns of UV-absorbing pigments are controlled by a newly identified regulatory region and may be under the influence of environmental factors.
In the common sunflower, patterns of UV-absorbing pigments are controlled by a newly identified regulatory region and may be under the influence of environmental factors.
Topics: Color; Flowers; Helianthus; Pigmentation
PubMed: 35061584
DOI: 10.7554/eLife.76105 -
BMC Ecology and Evolution Apr 2024Lizards of the genus Podarcis are widespread in the Mediterranean region, including islands and island archipelagos. These small-bodied lizards have a predominantly...
BACKGROUND
Lizards of the genus Podarcis are widespread in the Mediterranean region, including islands and island archipelagos. These small-bodied lizards have a predominantly protective green-brown colouration. However, some populations display unusual patterns, in which the colouration is predominantly blue or uniformly black. This study explores the factors that influence this chromatic variation, whether environmental (climate and island conditions) or evolutionary (phylogenetic trait conservatism). The colouration of 1400 individuals (27 species) was analysed in the CIELAB colour space.
RESULTS
Pagel's λ indicated that colouration is weakly conserved within phylogenetic lineages. Although the island surface plays a key role in the chromatic variability of these lacertids, geographic isolation and climate hold less influence. The colouration of some small island populations tends to be uniform and dark, possibly due to intense intraspecific competition and lower predatory pressure.
CONCLUSIONS
This study highlights the importance of island populations in understanding the processes that favour the emergence of extreme phenotypes in small ectothermic vertebrates.
Topics: Lizards; Animals; Mediterranean Region; Color; Pigmentation; Phylogeny; Islands; Climate; Biological Evolution; Phenotype; Environment
PubMed: 38658833
DOI: 10.1186/s12862-024-02242-1 -
Cell Reports Jan 2022Melanocytes, the pigment-producing cells, are replenished from multiple stem cell niches in adult tissue. Although pigmentation traits are known risk factors for...
Melanocytes, the pigment-producing cells, are replenished from multiple stem cell niches in adult tissue. Although pigmentation traits are known risk factors for melanoma, we know little about melanocyte stem cell (McSC) populations other than hair follicle McSCs and lack key lineage markers with which to identify McSCs and study their function. Here we find that Tfap2b and a select set of target genes specify an McSC population at the dorsal root ganglia in zebrafish. Functionally, Tfap2b is required for only a few late-stage embryonic melanocytes, and is essential for McSC-dependent melanocyte regeneration. Fate mapping data reveal that tfap2b McSCs have multifate potential, and are the cells of origin for large patches of adult melanocytes, two other pigment cell types (iridophores and xanthophores), and nerve-associated cells. Hence, Tfap2b confers McSC identity in early development, distinguishing McSCs from other neural crest and pigment cell lineages, and retains multifate potential in the adult zebrafish.
Topics: Animals; Cell Differentiation; Cell Lineage; Melanocytes; Pigmentation; Skin; Skin Pigmentation; Stem Cells; Transcription Factor AP-2; Zebrafish; Zebrafish Proteins
PubMed: 35021087
DOI: 10.1016/j.celrep.2021.110234 -
BMC Biology May 2023Gene duplication events are critical for the evolution of new gene functions. Aristaless is a major regulator of distinct developmental processes. It is most known for...
BACKGROUND
Gene duplication events are critical for the evolution of new gene functions. Aristaless is a major regulator of distinct developmental processes. It is most known for its role during appendage development across animals. However, more recently other distinct biological functions have been described for this gene and its duplicates. Butterflies and moths have two copies of aristaless, aristaless1 (al1) and aristaless2 (al2), as a result of a gene duplication event. Previous work in Heliconius has shown that both copies appear to have novel functions related to wing color patterning. Here we expand our knowledge of the expression profiles associated with both ancestral and novel functions of Al1 across embryogenesis and wing pigmentation. Furthermore, we characterize Al2 expression, providing a comparative framework between gene copies within the same species, allowing us to understand the origin of new functions following gene duplication.
RESULTS
Our work shows that the expression of both Al1 and Al2 is associated with the ancestral function of sensory appendage (leg, mouth, spines, and eyes) development in embryos. Interestingly, Al1 exhibits higher expression earlier in embryogenesis while the highest levels of Al2 expression are shifted to later stages of embryonic development. Furthermore, Al1 localization appears extranuclear while Al2 co-localizes tightly with nuclei earlier, and then also expands outside the nucleus later in development. Cellular expression of Al1 and Al2 in pupal wings is broadly consistent with patterns observed during embryogenesis. We also describe, for the first time, how Al1 localization appears to correlate with zones of anterior/posterior elongation of the body during embryonic growth, showcasing a possible new function related to Aristaless' previously described role in appendage extension.
CONCLUSIONS
Overall, our data suggest that while both gene copies play a role in embryogenesis and wing pigmentation, the duplicates have diverged temporally and mechanistically across those functions. Our study helps clarify principles behind sub-functionalization and gene expression evolution associated with developmental functions following gene duplication events.
Topics: Animals; Butterflies; Pigmentation; Wings, Animal
PubMed: 37170114
DOI: 10.1186/s12915-023-01602-5 -
Current Biology : CB Feb 2018The bright yellow, green and red feathers of parrots depend on unique pigments termed 'psittacofulvins'. The discovery of a gene underlying psittacofulvin colouration...
The bright yellow, green and red feathers of parrots depend on unique pigments termed 'psittacofulvins'. The discovery of a gene underlying psittacofulvin colouration shows that this evolutionary innovation was achieved by co-opting an existing gene into feather development.
Topics: Animals; Color; Melopsittacus; Parrots; Pigmentation; Pigments, Biological
PubMed: 29408256
DOI: 10.1016/j.cub.2017.12.045 -
Insect Biochemistry and Molecular... May 2018The chemical composition of the scale insect Dactylopius coccus was analyzed with the aim to discover new possible intermediates in the biosynthesis of carminic acid....
The chemical composition of the scale insect Dactylopius coccus was analyzed with the aim to discover new possible intermediates in the biosynthesis of carminic acid. UPLC-DAD/HRMS analyses of fresh and dried insects resulted in the identification of three novel carminic acid analogues and the verification of several previously described intermediates. Structural elucidation revealed that the three novel compounds were desoxyerythrolaccin-O-glucosyl (DE-O-Glcp), 5,6-didehydroxyerythrolaccin 3-O-β-D-glucopyranoside (DDE-3-O-Glcp), and flavokermesic acid anthrone (FKA). The finding of FKA in D. coccus provides solid evidence of a polyketide, rather than a shikimate, origin of coccid pigments. Based on the newly identified compounds, we present a detailed biosynthetic scheme that accounts for the formation of carminic acid (CA) in D. coccus and all described coccid pigments which share a flavokermesic acid (FK) core. Detection of coccid pigment intermediates in members of the Planococcus (mealybugs) and Pseudaulacaspis genera shows that the ability to form these pigments is taxonomically more widely spread than previously documented. The shared core-FK-biosynthetic pathway and wider taxonomic distribution suggests a common evolutionary origin for the trait in all coccid dye producing insect species.
Topics: Animals; Carmine; Hemiptera; Pigmentation
PubMed: 29551461
DOI: 10.1016/j.ibmb.2018.03.002 -
PLoS Genetics Feb 2021Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present...
Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.
Topics: Animals; Chromatophores; Columbidae; Eye Color; Gene Expression Profiling; Genome-Wide Association Study; Genomics; Glucose Transport Proteins, Facilitative; Iris; Mutation; Pigmentation; RNA Stability; Skin Pigmentation; Vertebrates; Whole Genome Sequencing
PubMed: 33621224
DOI: 10.1371/journal.pgen.1009404 -
Archives of Pathology & Laboratory... Mar 2017- Colors are important to all living organisms because they are crucial for camouflage and protection, metabolism, sexual behavior, and communication. Human organs... (Review)
Review
CONTEXT
- Colors are important to all living organisms because they are crucial for camouflage and protection, metabolism, sexual behavior, and communication. Human organs obviously have color, but the underlying biologic processes that dictate the specific colors of organs and tissues are not completely understood. A literature search on the determinants of color in human organs yielded scant information.
OBJECTIVES
- To address 2 specific questions: (1) why do human organs have color, and (2) what gives normal and pathologic tissues their distinctive colors?
DATA SOURCES
- Endogenous colors are the result of complex biochemical reactions that produce biologic pigments: red-brown cytochromes and porphyrins (blood, liver, spleen, kidneys, striated muscle), brown-black melanins (skin, appendages, brain nuclei), dark-brown lipochromes (aging organs), and colors that result from tissue structure (tendons, aponeurosis, muscles). Yellow-orange carotenes that deposit in lipid-rich tissues are only produced by plants and are acquired from the diet. However, there is lack of information about the cause of color in other organs, such as the gray and white matter, neuroendocrine organs, and white tissues (epithelia, soft tissues). Neoplastic tissues usually retain the color of their nonneoplastic counterpart.
CONCLUSIONS
- Most available information on the function of pigments comes from studies in plants, microorganisms, cephalopods, and vertebrates, not humans. Biologic pigments have antioxidant and cytoprotective properties and should be considered as potential future therapies for disease and cancer. We discuss the bioproducts that may be responsible for organ coloration and invite pathologists and pathology residents to look at a "routine grossing day" with a different perspective.
Topics: Animals; Humans; Pathology; Pigmentation
PubMed: 28234573
DOI: 10.5858/arpa.2016-0274-SA -
Traffic (Copenhagen, Denmark) Apr 2019The mechanisms that regulate skin pigmentation have been the subject of intense research in recent decades. In contrast with melanin biogenesis and transport within...
The mechanisms that regulate skin pigmentation have been the subject of intense research in recent decades. In contrast with melanin biogenesis and transport within melanocytes, little is known about how melanin is transferred and processed within keratinocytes. Several models have been proposed for how melanin is transferred, with strong evidence supporting coupled exo/endocytosis. Recently, two reports suggest that upon internalization, melanin is stored within keratinocytes in an arrested compartment, allowing the pigment to persist for long periods. In this commentary, we identify a striking parallelism between melanin processing within keratinocytes and the host-pathogen interaction with Plasmodium, opening new avenues to understand the complex molecular mechanisms that ensure skin pigmentation and photoprotection.
Topics: Host-Pathogen Interactions; Keratinocytes; Melanins; Melanocytes; Skin Pigmentation
PubMed: 30801937
DOI: 10.1111/tra.12638