The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes.

Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

Use-dependent plasticity explains aftereffects in visually guided locomotor learning of a novel step length asymmetry.

Studies of upper extremity reaching show that use-dependent plasticity, or learning from repetition, plays an important role in shaping motor behaviors. Yet the impact of repetition on locomotor learning is unclear, despite the fact that gait is developed and practiced over millions of repetitions. To test whether repetition alone can induce storage of a novel walking pattern, we instructed two groups of young healthy subjects to learn an asymmetric walking pattern through two distinct learning paradigms. The first group learned a new pattern through an established visual distortion paradigm, which provided both sensory prediction error and repetition of movement patterns to induce walking aftereffects, and the second received veridical feedback with a target change, which provided only repetition (use-dependent plasticity) to induce aftereffects. When feedback was removed, both groups demonstrated aftereffects in the primary outcome, step asymmetry index. Surprisingly, despite the different task demands, both groups produced similar aftereffect magnitudes, which also had similar rates of decay, suggesting that the addition of sensory prediction errors did not improve storage of learning beyond that induced by the use-dependent process alone. To further characterize the use-dependent process, we conducted a second experiment to quantify aftereffect size in a third group who practiced double the asymmetry magnitude. This new group showed a proportionately greater magnitude of the use-dependent aftereffect. Together, these findings show that the primary driver of storage of a new step length asymmetry during visually guided locomotor learning is repetition, not sensory prediction error, and this effect scales with the learning magnitude.NEW & NOTEWORTHY Use-dependent plasticity, or learning from repetition, is an important process for upper extremity reaching tasks, but its contribution to walking is not well established. Here, we demonstrate the existence of a dose-dependent, use-dependent process during visually guided treadmill walking. We also show that sensory prediction errors, previously thought to drive aftereffects in similar locomotor learning paradigms, do not appear to play a significant role in visually driven learning of a novel step asymmetry during treadmill walking.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

The pig X and Y Chromosomes: structure, sequence, and evolution.

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Reinforcement Learning during Locomotion.

When learning a new motor skill, people often must use trial and error to discover which movement is best. In the reinforcement learning framework, this concept is known as exploration and has been linked to increased movement variability in motor tasks. For locomotor tasks, however, increased variability decreases upright stability. As such, exploration during gait may jeopardize balance and safety, making reinforcement learning less effective. Therefore, we set out to determine if humans could acquire and retain a novel locomotor pattern using reinforcement learning alone. Young healthy male and female participants walked on a treadmill and were provided with binary reward feedback (indicated by a green checkmark on the screen) that was tied to a fixed monetary bonus, to learn a novel stepping pattern. We also recruited a comparison group who walked with the same novel stepping pattern but did so by correcting for target error, induced by providing real-time veridical visual feedback of steps and a target. In two experiments, we compared learning, motor variability, and two forms of motor memories between the groups. We found that individuals in the binary reward group did, in fact, acquire the new walking pattern by exploring (increasing motor variability). Additionally, while reinforcement learning did not increase implicit motor memories, it resulted in more accurate explicit motor memories compared with the target error group. Overall, these results demonstrate that humans can acquire new walking patterns with reinforcement learning and retain much of the learning over 24 h.

Individuals early after anterior cruciate ligament reconstruction show intact motor learning of step length via the split-belt treadmill.

BACKGROUND: Rupturing the anterior cruciate ligament is an orthopedic injury that results in neuromuscular impairments affecting sensory input to the central nervous system. Traditional physical therapy after anterior cruciate ligament reconstruction aims to rehabilitate orthopedic impairments but fails to address asymmetric gait mechanics that are present post-operatively and are linked to the development of post-traumatic osteoarthritis. A first step towards developing gait interventions is understanding if individuals after anterior cruciate ligament reconstruction have the capacity to learn new walking mechanics. METHODS: The split-belt treadmill offers a task-specific approach to examine neuromuscular adaptations in patients after injury. The potential for changing spatiotemporal gait mechanics via split-belt treadmill adaptation has not been tested early after anterior cruciate ligament reconstruction; nor has the ability to retain and transfer newly learned gait mechanics. Therefore, we used a split-belt treadmill paradigm to compare gait adaptation, retention, and transfer to overground walking between 15 individuals 3-9 months after anterior cruciate ligament reconstruction and 15 matched control individuals. FINDINGS: Results suggested individuals after anterior cruciate ligament reconstruction were able to adapt and retain step length symmetry changes as well as controls. There was also evidence of partial transfer to overground walking, similar to controls. INTERPRETATION: Despite disruption in afferent feedback from the joint, individuals early after anterior cruciate ligament reconstruction can learn a new gait pattern using sensorimotor adaptation, retain, and partially transfer the learned gait pattern. This may be a critical time to intervene with gait-specific interventions targeting post-operative gait asymmetries.

Explicit and implicit locomotor learning in individuals with chronic hemiparetic stroke.

Motor learning involves both explicit and implicit processes that are fundamental for acquiring and adapting complex motor skills. However, stroke may damage the neural substrates underlying explicit and/or implicit learning, leading to deficits in overall motor performance. While both learning processes are typically used in concert in daily life and rehabilitation, no gait studies have determined how these processes function together after stroke when tested during a task that elicits dissociable contributions from both. Here, we compared explicit and implicit locomotor learning in individuals with chronic stroke to age- and sex-matched neurologically intact controls. We assessed implicit learning using split-belt adaptation (where two treadmill belts move at different speeds). We assessed explicit learning (i.e., strategy-use) using visual feedback during split-belt walking to help individuals explicitly correct for step length errors created by the split-belts. The removal of visual feedback after the first 40 strides of split-belt walking, combined with task instructions, minimized contributions from explicit learning for the remainder of the task. We utilized computational modeling to determine the individual contributions of explicit and implicit processes to overall behavioral change. The computational and behavioral analyses revealed that, compared to controls, individuals with chronic stroke demonstrated deficits in both explicit and implicit contributions to locomotor learning, a result that runs counter to prior work testing each process individually during gait. Since post-stroke locomotor rehabilitation involves interventions that rely on both explicit and implicit motor learning, future work should determine how locomotor rehabilitation interventions can be structured to optimize overall motor learning.

Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis.

The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.

Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution.

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population's transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how 'adaptation begets adaptation'; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.

Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes. The NCBI genome annotation pipeline identified 39,091 genes, 19,819 of them protein-coding. We also identified segmental duplications, inferred GO term annotations, and computed orthologs of human and mouse genes. This reference-quality genome will be an important resource for research on mammalian development, metabolism, and body size control.

Evolution and genetic architecture of sex-limited polymorphism in cuckoos.

Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (Cuculus canorus) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species. Here, we show that female plumage dichromatism maps to the female-restricted genome. We further demonstrate that, consistent with balancing selection, ancestry of the rufous phenotype is shared with the likewise female dichromatic sister species, the oriental cuckoo (Cuculus optatus). This study shows that sex-specific polymorphism in trait variation can be resolved by genetic variation residing on a sex-limited chromosome and be maintained across species boundaries.

A reliable and efficient adaptive Bayesian method to assess static lower limb position sense.

Background: Lower limb proprioception is critical for maintaining stability during gait and may impact how individuals modify their movements in response to changes in the environment and body state, a process termed "sensorimotor adaptation". However, the connection between lower limb proprioception and sensorimotor adaptation during human gait has not been established. We suspect this gap is due in part to the lack of reliable, efficient methods to assess global lower limb proprioception in an ecologically valid context. New Method: We assessed static lower limb proprioception using an alternative forced choice task, administered twice to determine test-retest reliability. Participants stood on a dual-belt treadmill which passively moved one limb to stimulus locations selected by a Bayesian adaptive algorithm. At the stimulus locations, participants judged relative foot positions and the algorithm estimated the point of subjective equality (PSE) and the uncertainty of lower limb proprioception. Results: Using the Bland-Altman method, combined with Bayesian statistics, we found that both the PSE and uncertainty estimates had good reliability. Comparison with Existing Methods: Current methods assessing static lower limb proprioception do so within a single joint, in non-weight bearing positions, and rely heavily on memory. One exception assessed static lower limb proprioception in standing but did not measure reliability and contained confounds impacting participants' judgments, which we experimentally controlled here. Conclusions: This efficient and reliable method assessing lower limb proprioception will aid future mechanistic understanding of locomotor adaptation and serve as a useful tool for basic and clinical researchers studying balance and falls.

A reliable and efficient adaptive Bayesian method to assess static lower limb position sense.

BACKGROUND: Lower limb proprioception is critical for maintaining stability during gait and may impact how individuals modify their movements in response to changes in the environment and body state, a process termed "sensorimotor adaptation". However, the connection between lower limb proprioception and sensorimotor adaptation during human gait has not been established. We suspect this gap is due in part to the lack of reliable, efficient methods to assess global lower limb proprioception in an ecologically valid context. NEW METHOD: We assessed static lower limb proprioception using an alternative forced choice task, administered twice to determine test-retest reliability. Participants stood on a dual-belt treadmill which passively moved one limb to stimulus locations selected by a Bayesian adaptive algorithm. At the stimulus locations, participants judged relative foot positions and the algorithm estimated the point of subjective equality (PSE) and the uncertainty of lower limb proprioception. RESULTS: Using the Bland-Altman method, combined with Bayesian statistics, we found that both the PSE and uncertainty estimates had good reliability. COMPARISON WITH EXISTING METHOD(S): Current methods assessing static lower limb proprioception do so within a single joint, in non-weight bearing positions, and rely heavily on memory. One exception assessed static lower limb proprioception in standing but did not measure reliability and contained confounds impacting participants' judgments, which we experimentally controlled here. CONCLUSIONS: This efficient and reliable method assessing lower limb proprioception will aid future mechanistic understanding of locomotor adaptation and serve as a useful tool for basic and clinical researchers studying balance and falls.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti, Evans, 1925.

We present a genome assembly from an individual male Anopheles moucheti (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 271 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length.

The Consistency of Prior Movements Shapes Locomotor Use-Dependent Learning.

Repetition is an indispensable component of motor skill acquisition. However, it is unknown how consistent repeated movement patterns must be to engage an implicit "use-dependent" learning mechanism. In this Registered Report, we tackled this question through a combination of computational modeling, simulations, and behavioral experiments involving visually-guided treadmill walking. Our hypotheses were formalized by two distinct computational models: in the two-process Strategy plus Use-Dependent model, use-dependent learning is viewed as a slowly updating and slowly decaying bias in the direction of repeated movements. The Adaptive Bayesian model frames use-dependent learning as an emergent property of quickly adapting prior probabilities of target step lengths. Critically, the Adaptive Bayesian model is much more sensitive to variable practice than the Strategy plus Use-Dependent model. To test these hypotheses, human participants (N = 18, 10 females) learned a novel asymmetric stepping pattern under three conditions with differing amounts of practice consistency during a learning block. We probed use-dependent movement biases immediately postlearning by asking participants to "walk normally" during a washout block with no visual feedback (VF). We found that the total magnitude of use-dependent learning depended on practice consistency during learning, consistent with the Adaptive Bayesian model. However, this dependence faded quickly as biases became similar in magnitude over subsequent strides across all conditions, an observation more consistent with the Strategy plus Use-Dependent model. Simple post hoc adjustments to the Strategy plus Use-Dependent model made clear that these seemingly opposing effects of practice consistency can result from a unitary use-dependent learning process shaped by recent movement history.

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.).

Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).

BACKGROUND: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. FINDINGS: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. CONCLUSIONS: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.