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1. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai , Drosophila takahashii , Drosophila bipectinata , and Drosophila ananassae

   https://doi.org/10.1093/g3journal/jkad191  

   Leung, Wilson; Torosin, Nicole; Cao, Weihuan; Reed, Laura K; Arrigo, Cindy; Elgin, Sarah C; Ellison, Christopher E (August 2023, G3: Genes, Genomes, Genetics)

   Vogel, K (Ed.)

   Abstract Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion. 

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2. The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

   https://doi.org/10.1093/gbe/evab262  

   Cerca, José; Armstrong, Ellie E; Vizueta, Joel; Fernández, Rosa; Dimitrov, Dimitar; Petersen, Bent; Prost, Stefan; Rozas, Julio; Petrov, Dmitri; Gillespie, Rosemary G (December 2021, Genome Biology and Evolution)

   Gossmann, Toni (Ed.)

   Abstract Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion. 

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3. AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation

   https://doi.org/https://doi.org/10.1101/2021.07.29.454331  

   Song, B; Marco-Sola, S; Moreto, M; Johnson, LC; Bucker, ES; Stitzer, MC (July 2021, bioRxiv)

   null (Ed.)

   Millions of species are currently being sequenced and their genomes are being compared. Many of them have more complex genomes than model systems and raised novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication or polyploidy levels. Here we introduce AnchorWave, which performs whole-genome duplication informed collinear anchor identification between genomes and performs base-pair resolution global alignments for collinear blocks using the wavefront algorithm and a 2-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multi-kilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs between two maize lines. By contrast, other genome alignment tools showed almost zero power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome than the closest competitive approach, when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor binding sites (TFBSs) at a rate of 1.05-74.85 fold higher than other tools, while with significantly lower false positive alignments. AnchorWave shows obvious improvement when applied to genomes with dispersed repeats, active transposable elements, high sequence diversity and whole-genome duplication variation. 

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4. Substantial structural variation and repetitive DNA content contribute to intraspecific plastid genome evolution

   https://doi.org/10.1186/s12864-025-11525-w  

   López-Caamal, Alfredo; Gandee, Tyler; Galloway, Laura F; Barnard-Kubow, Karen B (April 2025, BMC Genomics)

   Background Plastids have highly conserved genomes in most land plants. However, in several families, plastid genomes exhibit high rates of nucleotide substitution and structural rearrangements among species. This elevated rate of evolution has been posited to lead to increased rates of plastid-nuclear incompatibilities (PNI), potentially acting as a driver of speciation. However, the extent to which plastid structural variation exists within a species is unknown. This study investigates whether plastid structural variation, observed at the interspecific level in Campanulaceae, also occurs within Campanula americana, a species with strong intraspecific PNI. We assembled multiple plastid genomes from three lineages of C. americana that exhibit varying levels of PNI when crossed. We then investigated the structural variation and repetitive DNA content among these lineages and compared the repetitive DNA content with that of other species within the family. Results We found significant variation in plastid genome size among the lineages of C. americana (188,309–201,788 bp). This variation was due in part to multiple gene duplications in the inverted repeat region. Lineages also varied in their repetitive DNA content, with the Appalachian lineage displaying the highest proportion of tandem repeats (~ 10%) compared to the Eastern and Western lineages (~ 6%). In addition, genes involved in transcription and protein transport showed elevated sequence divergence between lineages, and a strong correlation was observed between genome size and repetitive DNA content. Campanula americana was found to have one of the most repetitive plastid genomes within Campanulaceae. Conclusions These findings challenge the conventional view of plastid genome conservation within a species and suggest that structural variation, differences in repetitive DNA content, and divergence of key genes involved in transcription and protein transport may play a role in PNI. This study highlights the need for further research into the genetic mechanisms underlying PNI, a key process in the early stages of speciation. 

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5. Using Oxford Nanopore MinION sequencing runs to identify genes from across a diverse set of monogonont rotifers

   MOHL, Jonathon EY; HOCHBERG, Rick; WALLACE, Robert L; LAVRETSKY, Philip; WALSH, Elizabeth J (September 2022, The International Rotifer Symposium - ROTIFERA XVI)

   Determining the genomic content of a diverse group of monogonont rotifers can provide an understanding of their genetic divergence, and infom1ation required to develop a more complete phylogenetic reconstruction. Although the number of monogonont genomes sequenced has recently increased, most of that work has been in the context of ecotoxicology and/or stress responses, and most have focused on Brachionus spp. To expand knowledge of rotifer genomic diversity, we sequenced eight non-brachionid monogononts using long read Oxford Nanopore MinION technology and found increased yields when coupled with QuantBio AccuStart Long Range Taq polymerase during PCR whole-genome fragment amplification. Subsequently, sequences were assembled using Flye, polished with Racon and then filtered to a minimum length of 1,000 bases. Braker was used to identify predicted coding regions that were then assigned functional annotations by Blast2GO. Quast and Busco were used to check assembly and protein calling, respectively. Taxa were sequenced in a single run to an average of 14 billion bases and with N50 read lengths ranging from 1,673 to 4,586 bases. Genome assembly sizes ranged from 39.0 Mb (Hexrathra sp.) to 216.9 Mb (Plationus patulus) with the largest scaffolds averaging 1.9 Mb across the taxa. Braker identified 11,162 to 36,699 proteins in the respective smallest and largest assembled genomes. Complete BUSCO scores averaged 92% across the taxa. Our work, along with previously published studies, will allow comparisons of multiple genetic pathways within Rotifera, including those related to reproductive processes (i.e., switching between mitosis and meiosis, amphoterism, and male dwarfism). 

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