Dr. Soumia Benallag completed her neurosurgical residency at Mustapha Bacha Hospital in Algiers and is currently an attending neurosurgeon at Bachir Benacer Hospital in Biskra, Algeria. Her fellowship will be at the Barrow Neurological Institute in Phoenix, Arizona under the guidance of Dr. Michael Lawton. During her fellowship, Dr. Benallag will be able to observe complex neurosurgical procedures, participate in daily film review teaching rounds, attend weekly Neurosurgery Clinical Conferences and Neurosurgery/Neurology Grand Rounds, as well as a variety of other Neuroscience Lectures and Conferences that are hosted throughout the year.

The most recent assembly of D. miranda was generated via short-read Illumina sequencing and is highly fragmented. In particular, the genome was in 47,035 scaffolds, with a scaffold N50 (a weighted median statistic such that 50% of the entire assembly is contained in scaffolds equal to or larger than this value) of 5,007 bp and a total assembled genome size of 112 Mb (a female-only assembly resulted in 22,259 scaffolds, with an N50 of 13,773 bp and an assembled size of 125 Mb). The high amount of sequence similarity between the neo-sex chromosomes (98.5% identical at the nucleotide level), yet high repeat content of the neo-Y (over 50% of its DNA is derived from repeats [19]) posed a particular challenge to its assembly using short reads. Specifically, initial attempts to assemble the neo-Y resulted in a chimeric, highly fragmented and incomplete assembly, consisting of 36,282 (often chimeric) scaffolds, and a scaffold N50 of only 715 bp [20]. Thus, our previous analysis of neo-Y chromosome gene content evolution was instead based on mapping male reads to the neo-X assembly and identifying male-specific SNPs [20], or trying to reconstruct neo-Y transcripts using both male and female genome and transcriptome data [21]. This indirect approach, however, only allows the investigation of conserved regions on the neo-sex chromosome that differ by simple SNPs or short indels within genes. Here, we assemble the genome of D. miranda using long reads for contig formation, short reads for consensus validation, and scaffolding by chromatin interaction mapping, and we verify our assembly using optical maps and BAC clone sequencing. Our assembly covers large fractions of repetitive DNA, with entire chromosomes being in a single scaffold, including their centromeres, and we recover over >100 Mb of the recently formed neo-Y chromosome. Our new assembly strategy achieves superior continuity and accuracy and provides a new standard reference for the investigation of repetitive sequences and Y chromosome evolution in this species.

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To maximize accuracy of the final reference assembly, errors were manually curated before final gap filling and polishing (S2 Table). Our final assembly, D.mir2.0, totaled 287 Mb of sequence, with a scaffold NG50 of 35.3 Mb (Table 1). D.mir2.0 comprises just 102 scaffolds and 120 gaps (S7 Table), and the three autosomes, the three X chromosome arms, and the Y of D. miranda are all mostly covered by a single scaffold (Fig 3). The unplaced scaffolds are relatively small (median size 37.3 kb) and highly repeat-rich (median repeat content 94.7%), and sex-specific coverage patterns suggest that most are derived from the Y chromosome. In contrast, the previous assembly D.mir1.0 consisted of 47,035 scaffolds [20]. We used two approaches, REPdenovo [26] and RepeatModeler [27], to annotate repeats in the D. miranda genome and Maker [28] to annotate genes (Fig 3). We identified a total of 17,745 genes, and 43.7% of the genome was annotated as repeats. BUSCO assessments [29] support that our genome assembly and annotation are highly complete (S8 Table). 589ccfa754

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