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1. Genome Assembly of the Dogface Butterfly Zerene cesonia

   https://doi.org/10.1093/gbe/evz254  

   Rodriguez-Caro, Luis ; Fenner, Jennifer ; Benson, Caleb ; Van Belleghem, Steven M ; Counterman, Brian A ; Eyre-Walker, Adam ( January 2020 , Genome Biology and Evolution)

   Abstract Comparisons of high-quality, reference butterfly, and moth genomes have been instrumental to advancing our understanding of how hybridization, and natural selection drive genomic change during the origin of new species and novel traits. Here, we present a genome assembly of the Southern Dogface butterfly, Zerene cesonia (Pieridae) whose brilliant wing colorations have been implicated in developmental plasticity, hybridization, sexual selection, and speciation. We assembled 266,407,278 bp of the Z. cesonia genome, which accounts for 98.3% of the estimated 271 Mb genome size. Using a hybrid approach involving Chicago libraries with Hi-Rise assembly and a diploid Meraculous assembly, the final haploid genome was assembled. In the final assembly, nearly all autosomes and the Z chromosome were assembled into single scaffolds. The largest 29 scaffolds accounted for 91.4% of the genome assembly, with the remaining ∼8% distributed among another 247 scaffolds and overall N50 of 9.2 Mb. Tissue-specific RNA-seq informed annotations identified 16,442 protein-coding genes, which included 93.2% of the arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO). The Z. cesonia genome assembly had ∼9% identified as repetitive elements, with a transposable element landscape rich in helitrons. Similar to other Lepidoptera genomes, Z. cesonia showed a high conservation of chromosomal synteny. The Z. cesonia assembly provides a high-quality reference formore »studies of chromosomal arrangements in the Pierid family, as well as for population, phylo, and functional genomic studies of adaptation and speciation.« less
2. Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity

   https://doi.org/10.1038/s41598-018-38111-3  

   Gutierrez-Gonzalez, Juan J. ; Mascher, Martin ; Poland, Jesse ; Muehlbauer, Gary J. ( February 2019 , Scientific Reports)

   Wheat (Triticum aestivum) genetic maps are a key enabling tool for genetic studies. We used genotyping-by-sequencing-(GBS) derived markers to map recombinant inbred line (RIL) and doubled haploid (DH) populations from crosses of W7984 by Opata, and used the maps to explore features of recombination control. The RIL and DH populations, SynOpRIL and SynOpDH, were composed of 906 and 92 individuals, respectively. Two high-density genetic linkage framework maps were constructed of 2,842 and 2,961 cM, harboring 3,634 and 6,580 markers, respectively. Using imputation, we added 43,013 and 86,042 markers to the SynOpRIL and SynOpDH maps. We observed preferential recombination in telomeric regions and reduced recombination in pericentromeric regions. Recombination rates varied between subgenomes, with the D genomes of the two populations exhibiting the highest recombination rates of 0.26–0.27 cM/Mb. QTL mapping identified two additive and three epistatic loci associated with crossover number. Additionally, we used published POPSEQ data from SynOpDH to explore the structural variation in W7984 and Opata. We found that chromosome 5AS is missing from W7984. We also found 2,332 variations larger than 100 kb. Structural variants were more abundant in distal regions, and overlapped 9,196 genes. The two maps provide a resource for trait mapping and genomic-assisted breeding.
3. Female flowers first: QTL mapping in eastern black walnut (Juglans nigra L.) identifies a dominant locus for heterodichogamy syntenic with that in Persian walnut (J. regia L.)

   https://doi.org/10.1007/s11295-022-01580-9  

   Chatwin, Warren ; Shirley, Devin ; Lopez, Jacqueline ; Sarro, Joseph ; Carlson, John ; Devault, Alison ; Pfrender, Mike ; Revord, Ronald ; Coggeshall, Mark ; Romero-Severson, Jeanne ( December 2022 , Tree Genetics & Genomes)

   Eastern black walnut (Juglans nigraL.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F₁full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping inJ. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regiaL.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to theJ. regia“Chandler” V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparisonmore »of this and subsequentJ. nigramaps and otherJuglandaceaegenetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

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4. OMGS: Optical Map-based Genome Scaffolding

   https://doi.org/10.1007/978-3-030-17083-7_12  

   W. Pan, T. Jiang ( January 2019 , RECOMB 2019 - ACM Annual Conference on Research in Computational Molecular Biology)

   Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this paper, we introduce a novel scaffolding algorithm called OMGS that for the first time can take advantages of multiple optical maps. OMGS solves several optimization problems to generate scaffolds with optimal contiguity and correctness. Extensive experimental results demonstrate that our tool outperforms existing methods when multiple optical maps are available, and produces comparable scaffolds using a single optical map. OMGS can be obtainedmore »from GIT.« less
5. Rapid Evolution of the Fine-scale Recombination Landscape in Wild House Mouse ( Mus musculus ) Populations

   https://doi.org/10.1093/molbev/msac267  

   Wooldridge, Lydia K ; Dumont, Beth L ( January 2023 , Molecular Biology and Evolution)

   Falush, Daniel (Ed.)

   Abstract Meiotic recombination is an important evolutionary force and an essential meiotic process. In many species, recombination events concentrate into hotspots defined by the site-specific binding of PRMD9. Rapid evolution of Prdm9's zinc finger DNA-binding array leads to remarkably abrupt shifts in the genomic distribution of hotspots between species, but the question of how Prdm9 allelic variation shapes the landscape of recombination between populations remains less well understood. Wild house mice (Mus musculus) harbor exceptional Prdm9 diversity, with >150 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct broad- and fine-scale sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence formore »population-specific differences in the degree and direction of sex dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in M. musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations.« less