Black raspberry (
Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of
- Award ID(s):
- 1933521
- NSF-PAR ID:
- 10216814
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Horticulture Research
- Volume:
- 8
- Issue:
- 1
- ISSN:
- 2662-6810
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Summary Rubus occidentalis ) is an important specialty fruit crop in theUS Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus ). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae andRubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca ) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein‐coding genes, we identified 290 very recent small‐scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberryF. vesca , which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed toVerticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and otherRubus cultivars. -
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Abstract Many lizard species face extinction due to worldwide climate change. The Guatemalan Beaded Lizard, Heloderma charlesbogerti, is a member of the Family Helodermatidae that may be particularly imperiled; fewer than 600 mature individuals are believed to persist in the wild. In addition, H. charlesbogerti lizards are phenotypically remarkable. They are large in size, charismatically patterned, and possess a venomous bite. Here, we report the draft genome of the Guatemalan Beaded Lizard using DNA from a wild-caught individual. The assembled genome totals 2.31 Gb in length, similar in size to the genomes of related species. Single-copy orthologs were used to produce a novel molecular phylogeny, revealing that the Guatemalan Beaded Lizard falls into a clade with the Asian Glass Lizard (Anguidae) and in close association with the Komodo Dragon (Varanidae) and the Chinese Crocodile Lizard (Shinisauridae). In addition, we identified 31,411 protein-coding genes within the genome. Of the genes identified, we found 504 that evolved with a differential constraint on the branch leading to the Guatemalan Beaded Lizard. Lastly, we identified a decline in the effective population size of the Guatemalan Beaded Lizard approximately 400,000 years ago, followed by a stabilization before starting to dwindle again 60,000 years ago. The results presented here provide important information regarding a highly endangered, venomous reptile that can be used in future conservation, functional genetic, and phylogenetic analyses.
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Hug, Laura A. (Ed.)ABSTRACT Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. “ Candidatus Accumulibacter phosphatis” (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage. IMPORTANCE “ Candidatus Accumulibacter phosphatis” is a model polyphosphate-accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the shared sequence identity of the polyphosphate kinase ( ppk1 ) locus. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen-cycling capabilities. However, such hypotheses have largely been made based on gene content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.more » « less
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Premise Male gametophytes of most seed plants deliver sperm to eggs via a pollen tube. Pollen tube growth rates (
PTGR s) of angiosperms are exceptionally rapid, a pattern attributed to more effective haploid selection under stronger pollen competition. Paradoxically, whole genome duplication (WGD ) has been common in angiosperms but rare in gymnosperms. Pollen tube polyploidy should initially acceleratePTGR because increased heterozygosity and gene dosage should increase metabolic rates. However, polyploidy should also independently increase tube cell size, causing more work which should decelerate growth. We asked how genome size changes have affected the evolution of seed plantPTGR s.Methods We assembled a phylogenetic tree of 451 species with known
PTGR s. We then used comparative phylogenetic methods to detect effects of neo‐polyploidy (within‐genus origins),DNA content, andWGD history onPTGR , and correlated evolution ofPTGR andDNA content.Results Gymnosperms had significantly higher
DNA content and slowerPTGR optima than angiosperms, and theirPTGR andDNA content were negatively correlated. For angiosperms, 89% of model weight favored Ornstein‐Uhlenbeck models with a fasterPTGR optimum for neo‐polyploids, whereasPTGR andDNA content were not correlated. For within‐genus and intraspecific‐cytotype pairs,PTGR s of neo‐polyploids < paleo‐polyploids.Conclusions Genome size increases should negatively affect
PTGR when genetic consequences ofWGD s are minimized, as found in intra‐specific autopolyploids (low heterosis) and gymnosperms (fewWGD s). But in angiosperms, the higherPTGR optimum of neo‐polyploids and non‐negativePTGR ‐DNA content correlation suggest that recurrentWGD s have caused substantialPTGR evolution in a non‐haploid state.
