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1. Nebulous without white : annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa

   https://doi.org/10.1093/g3journal/jkac231  

   Sottolano, Christopher J.; Revaitis, Nicole T.; Geneva, Anthony J.; Yakoby, Nir; Arbeitman, ed., M. (September 2022, G3 Genes|Genomes|Genetics)

   Abstract The diversity among Drosophila species presents an opportunity to study the molecular mechanisms underlying the evolution of biological phenomena. A challenge to investigating these species is that, unlike the plethora of molecular and genetics tools available for D. melanogaster research, many other species do not have sequenced genomes; a requirement for employing these tools. Selecting transgenic flies through white (w) complementation has been commonly practiced in numerous Drosophila species. While tolerated, the disruption of w is associated with impaired vision, among other effects in D. melanogaster. The D. nebulosa fly has a unique mating behavior which requires vision, and is thus unable to successfully mate in dark conditions. Here, we hypothesized that the disruption of w will impede mating success. As a first step, using PacBio long-read sequencing, we assembled a high-quality annotated genome of D. nebulosa. Using these data, we employed CRISPR/Cas9 to successfully disrupt the w gene. As expected, D. nebulosa males null for w did not court females, unlike several other mutant strains of Drosophila species whose w gene has been disrupted. In the absence of mating, no females became homozygous null for w. We conclude that gene disruption via CRISPR/Cas9 genome engineering is a successful tool in D. nebulosa, and that the w gene is necessary for mating. Thus, an alternative selectable marker unrelated to vision is desirable. 

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2. Haplotype Phased Chromosome-level Lycorma delicatula Genome and Annotation

   https://doi.org/10.6084/m9.figshare.28378361  

   Snead, Anthony; Meng, Fang; Largotta, Nicolas; Winchell, Kristin; Levine, Brenna A (January 2025, figshare)

   CitationSnead, A.A., Meng, F., Largotta, N. et al. Diploid chromosome-level genome assembly and annotation for Lycorma delicatula. Sci Data 12, 579 (2025). https://doi.org/10.1038/s41597-025-04854-8AbstractThe spotted lanternfly (Lycorma delicatula) is a planthopper species (Hemiptera: Fulgoridae) native to China but invasive in South Korea, Japan, and the United States where it is a significant threat to agriculture. Hence, genomic resources are critical to both management and understand the genomic characteristics of successful invaders. Here, we report a haplotype-phased genome assembly and annotation using PacBio long-read sequencing, Hi-C technology, and RNA-seq data. The 2.2 Gbp genome comprises 13 chromosomes, and our whole genome sequencing of eighty-two adults indicated chromosome four as the sex chromosome and anXO sex-determination system.We identified over 12,000 protein coding genes and performed functional annotation, facilitating identification of several candidate genes which may hold importance for spotted lanternfly control. Both the assemblies and annotations were highly complete with over 96% of BUSCO genes complete regardless of the database employed (i.e., Eukaryota, Arthropoda, Insecta). This reference-quality genome will serve as an important resource for both development and optimization of management practices for the spotted lanternfly and invasive genomics as a whole.Description of the data and file structureThis dataset contains the haplotype-phased chromosome-level genome assembly of the spotted lanternfly (Lycorma delicatula) described and published in Snead & Meng et al. (in review). The genome combined long-read data and HiC data (SRA31402152-SRA31402153) to assembly and scaffold each haplotype. The annotation uses RNAseq data from 12 adults (SRA31411873-SRA31411894) to structurally annotate both haplotypes. Finally, whole-genome sequencing of 82 adult spotted lanternfly (bioproject PRJNA1136004) described in the metadata csv provided was used to identify punitive sex chromosomes. The dataset also include GO results for each chromosome not explicitly described in the results of the manuscript.Files and variablesFile: SLF_Hap1.fastaDescription: A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 1 assembly.File: SLF_Hap2.fastaDescription: A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 2 assembly.File: SLF_Hap1_Repeats.gffDescription: A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 1 assembly.File: SLF_Hap2_Repeats.gffDescription: A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 2 assembly.File: SLF_Hap1.gffDescription: A structural annotation of the 13 chromosome haplotype 1 assembly with functional annotations.File: SLF_Hap2.gffDescription: A structural annotation of the 13 chromosome haplotype 2 assembly with functional annotations.File: GO_plot_chr_1.pngDescription: An image of the top 20 GO term results for chromosome 1.File: GO_plot_chr_2.pngDescription: An image of the top 20 GO term results for chromosome 2.File: GO_plot_chr_3.pngDescription: An image of the top 20 GO term results for chromosome 3.File: GO_plot_chr_8.pngDescription: An image of the top 20 GO term results for chromosome 8.File: GO_plot_chr_5.pngDescription: An image of the top 20 GO term results for chromosome 5.File: GO_plot_chr_4.pngDescription: An image of the top 20 GO term results for chromosome 4.File: GO_plot_chr_6.pngDescription: An image of the top 20 GO term results for chromosome 6.File: GO_plot_chr_7.pngDescription: An image of the top 20 GO term results for chromosome 7.File: GO_plot_chr_11.pngDescription: An image of the top 20 GO term results for chromosome 11.File: GO_plot_chr_9.pngDescription: An image of the top 20 GO term results for chromosome 9.File: GO_plot_chr_10.pngDescription: An image of the top 20 GO term results for chromosome 10.File: GO_plot_chr_12.pngDescription: An image of the top 20 GO term results for chromosome 12.File: GO_plot_chr_13.pngDescription: An image of the top 20 GO term results for chromosome 13.File: SLF_Samples_SRA.csvDescription: A csv with the sequencing information, SRA numbers, and sexes of the adults used in to identify the putative sex chromosome.File: SLF_RNAseq_Metadata.csvDescription: A csv with the sequencing information, SRA numbers, and other metadata for the RNAseq used to annotation the genomes.Variablesaccession: The SRA accession numberstudy: The studyobject_status: If the NCBI submission was new or not.bioproject_accession: The bioproject accession numberbiosample_accession: The Biosample accession numberlibrary_ID: The ID used to identify that genomic library.title: The title of the study (the bioproject)library_strategy: Specific sequencing technique used to prepare the library.library_source: The biological material used to create the sequencing library.library_selection: The library preparation method.library_layout: The arrangement of reads within the sequencing library.platform: The sequencing platform.instrument_model: The model of the sequences.design_description: Description of the study design.filetype: Type of filefilename: First filefilename2: Second filesex: The biological sex of the adult.Code/softwareThe initial haplotype-phased scaffolded genome was assembled by Dovetail Genomics (Cantata Bio) with standard software outlined in the methods with default settings. Scripts for the remaining work including annotation, gene ontology enrichment, and other analyses are located in the Github repository (https://github.com/anthonysnead/SLF-Genome-Assembly(opens in new window)).Access informationOther publicly accessible locations of the data:The raw sequencing data and the annotated haplotype-phased genome assembly of Lycorma delicatula have been deposited at the National Center for Biotechnology Information (NCBI). The Hi-C and HiFi data can be found under SRA31402152 and SRA31402153. The RNA-seq data can be found under SRA31411873-SRA31411894, while the DNA-seq data can be found under bioproject PRJNA1136004. 

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3. Genome balance and dosage effect drive allopolyploid formation in Brassica

   https://doi.org/10.1073/pnas.2217672120  

   Cao, Yao; Zhao, Kanglu; Xu, Junxiong; Wu, Lei; Hao, Fangyuan; Sun, Meiping; Dong, Jing; Chao, Getu; Zhang, Hong; Gong, Xiufeng; et al (April 2023, Proceedings of the National Academy of Sciences)

   Polyploidy is a major evolutionary force that has shaped plant diversity. However, the various pathways toward polyploid formation and interploidy gene flow remain poorly understood. Here, we demonstrated that the immediate progeny of allotriploid AACBrassica(obtained by crossing allotetraploidBrassica napusand diploidBrassica rapa) was predominantly aneuploids with ploidal levels ranging from near-triploidy to near-hexaploidy, and their chromosome numbers deviated from the theoretical distribution toward increasing chromosome numbers, suggesting that they underwent selection. Karyotype and phenotype analyses showed that aneuploid individuals containing fewer imbalanced chromosomes had higher viability and fertility. Within three generations of self-fertilization, allotriploids mainly developed into near or complete allotetraploids similar toB. napusvia gradually increasing chromosome numbers and fertility, suggesting that allotriploids could act as a bridge in polyploid formation, with aneuploids as intermediates. Self-fertilized interploidy hybrids ultimately generated new allopolyploids carrying different chromosome combinations, which may create a reproductive barrier preventing allotetraploidy back to diploidy and promote gene flow from diploids to allotetraploids. These results suggest that the maintenance of a proper genome balance and dosage drove the recurrent conversion of allotriploids to allotetraploids, which may contribute to the formation and evolution of polyploids. 

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4. Whole Genome Assembly and Annotation of Blackstripe Livebearer Poeciliopsis prolifica

   https://doi.org/10.1093/gbe/evad195  

   Zhang, Ying; Reynoso, Yuridia; Reznick, David; Wang, Xu (November 2023, Genome Biology and Evolution)

   Wheat, Christopher (Ed.)

   Abstract The blackstripe livebearer Poeciliopsis prolifica is a live-bearing fish belonging to the family Poeciliidae with high level of postfertilization maternal investment (matrotrophy). This viviparous matrotrophic species has evolved a structure similarly to the mammalian placenta. Placentas have independently evolved multiple times in Poeciliidae from nonplacental ancestors, which provide an opportunity to study the placental evolution. However, there is a lack of high-quality reference genomes for the placental species in Poeciliidae. In this study, we present a 674 Mb assembly of P. prolifica in 504 contigs with excellent continuity (contig N50 7.7 Mb) and completeness (97.2% Benchmarking Universal Single-Copy Orthologs [BUSCO] completeness score, including 92.6% single-copy and 4.6% duplicated BUSCO score). A total of 27,227 protein-coding genes were annotated from the merged datasets based on bioinformatic prediction, RNA sequencing and homology evidence. Phylogenomic analyses revealed that P. prolifica diverged from the guppy (Poecilia reticulata) ∼19 Ma. Our research provides the necessary resources and the genomic toolkit for investigating the genetic underpinning of placentation. 

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5. Complete Genome Sequences for Pseudomonas sp. Strains 29A and 43A

   https://doi.org/10.1128/MRA.00845-20  

   Baltrus, David A.; Clark, Meara; Humphrey, Parris T.; Whiteman, Noah K. (September 2020, Microbiology Resource Announcements)

   Thrash, J. Cameron (Ed.)

   ABSTRACT Pseudomonas sp. strains 29A and 43A were originally isolated from the phyllosphere of individual plants of Cardamine cordifolia (Brassicaceae). Here, we report complete genome sequences for these two closely related strains, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced on an Oxford Nanopore MinION flow cell. 

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