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BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Diabetic retinopathy is the most common microvascular complication of diabetes and is a major cause of blindness, but an understanding of the pathogenesis of the disease has been hampered by a lack of accurate animal models. Here, we explore the dynamics of retinal cellular changes in the Nile rat (Arvicanthis niloticus), a carbohydrate-sensitive model for type 2 diabetes. The early retinal changes in diabetic Nile rats included increased acellular capillaries and loss of pericytes that correlated linearly with the duration of diabetes. These vascular changes occurred in the presence of microglial infiltration but in the absence of retinal ganglion cell loss. After a prolonged duration of diabetes, the Nile rat also exhibits a spectrum of retinal lesions commonly seen in the human condition including vascular leakage, capillary non-perfusion, and neovascularization. Our longitudinal study documents a range and progression of retinal lesions in the diabetic Nile rat remarkably similar to those observed in human diabetic retinopathy, and suggests that this model will be valuable in identifying new therapeutic strategies.

Retinitis pigmentosa is the most common form of inherited blindness and can be caused by a multitude of different genetic mutations that lead to similar phenotypes. Specifically, mutations in ubiquitously expressed splicing factor proteins are known to cause an autosomal dominant form of the disease, but the retina-specific pathology of these mutations is not well understood. Fibroblasts from a patient with splicing factor retinitis pigmentosa caused by a missense mutation in the PRPF8 splicing factor were used to produce three diseased and three CRISPR/Cas9-corrected induced pluripotent stem cell (iPSC) clones. We differentiated each of these clones into retinal pigment epithelial (RPE) cells via directed differentiation and analyzed the RPE cells in terms of gene and protein expression, apicobasal polarity, and phagocytic ability. We demonstrate that RPE cells can be produced from patient-derived and corrected cells and they exhibit morphology and functionality similar but not identical to wild-type RPE cells in vitro. Functionally, the RPE cells were able to establish apicobasal polarity and phagocytose photoreceptor outer segments at the same capacity as wild-type cells. These data suggest that patient-derived iPSCs, both diseased and corrected, are able to differentiate into RPE cells with a near normal phenotype and without differences in phagocytosis, a result that differs from previous mouse models. These RPE cells can now be studied to establish a disease-in-a-dish system relevant to retinitis pigmentosa.

Shifts in the timing of life history events have become an important source of information about how organisms are responding to climate change. Phenological data have generally been treated as purely temporal, with scant attention to the inherent spatial aspects of such data. However, phenological data are tied to a specific location, and considerations of sampling design, both over space and through time, can critically affect the patterns that emerge. Focusing on flowering phenology, we describe how purely spatial shifts, such as adding new study plots, or the colonization of a study plot by a new species, can masquerade as temporal shifts. Such shifts can look like responses to climate change but are not. Furthermore, the same aggregate phenological curves can be composed of individuals with either very different or very similar phenologies. We conclude with a set of recommendations to avoid ambiguities arising from the spatiotemporal duality of phenological data.

Shifts in the timing of life history events have become an important source of information about how organisms are responding to climate change. Phenological data have generally been treated as purely temporal, with scant attention to the inherent spatial aspects of such data. However, phenological data are tied to a specific location, and considerations of sampling design, both over space and through time, can critically affect the patterns that emerge. Focusing on flowering phenology, we describe how purely spatial shifts, such as adding new study plots, or the colonization of a study plot by a new species, can masquerade as temporal shifts. Such shifts can look like responses to climate change but are not. Furthermore, the same aggregate phenological curves can be composed of individuals with either very different or very similar phenologies. We conclude with a set of recommendations to avoid ambiguities arising from the spatiotemporal duality of phenological data.

Citrus is one of the world's most important and widely produced fruit crops, with over a 100 million metric tons harvested from nearly 10 million hectares in 2023. Challenges in crop maintenance, production, and fruit quality necessitate developing new traits through Agrobacterium-mediated genetic transformation. While a few Agrobacterium strains (EHA105, GV3101, LBA4404) are known to transform citrus, many wild strains remain untested. We screened forty-one wild-type Agrobacterium strains isolated from various woody species and identified five capable of DNA transfer into citrus cells. Strain 1D1416 demonstrated the highest transient transformation frequency in Carrizo epicotyl explants (88%), outperforming the control EHA105 (84%) with comparable shoot regeneration rates (32% and 42%, respectively). Notably, 1D1416 exhibited no overgrowth and had the lowest necrosis and mortality rates in transformed tissues. It efficiently transferred the DsRed gene and induced galls in mature tissues of Mexican lime (70%), lemon (48%), Washington navel orange (25%), and clementine (6%). Genome sequencing of 1D1416 allowed for the disarming of the native T-DNA and addition of GAANTRY technology. This novel strain, combined with an optimized transformation procedure, make it a valuable tool for advancing citrus transformation. [ABSTRACT FROM AUTHOR]

Pollinators that collect pollen - and specifically, pollen-specialist bees - are often considered to be the best pollinators of a (host) plant. Although pollen collectors and pollen specialists often benefit host plants, especially in the pollen that they deliver (their pollination "effectiveness"), they can also exact substantial costs because they are motivated to collect as much pollen as possible, reducing the proportion of pollen removed that is subsequently delivered to stigmas (their pollination "efficiency"). From the plant perspective, pollen grains that do not pollinate conspecific stigmas are "wasted", and potentially costly. We measured costs and benefits of nectar-collecting, pollen-collecting, and pollen-specialist pollinator visitation to the spring ephemeral Claytonia virginica. Visits by the pollen-specialist bee Andrena erigeniae depleted pollen quickly and thoroughly. Although all pollinators delivered roughly the same number of grains, the pollen specialist contributed most to C. virginica pollen delivery because of high visitation rates. However, the pollen specialist also removed a large number of grains; this removal may be especially costly because it resulted in the depletion of pollen grains in C. virginica populations. While C. virginica appears to rely on pollen transfer by the pollen specialist in these populations, nectar-collecting visitors could provide the same benefit at a lower cost if their visitation rates increased. Pollen depletion affects a pollinator's value to plants, but is frequently overlooked. If they lower the effectiveness of future floral visitors, visits by A. erigeniae females to C. virginica may be more detrimental than beneficial compared to other pollinators and may, in some circumstances, reduce plant fitness rather than increase it. Therefore, A. erigeniae and C. virginica may vary in their degree of mutualism depending on the ecological context.