Redefining and interpreting genomic relationships of metafounders.

Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics-namely, heterozygosities, FST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy-Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form Γ b , b ' = 2 n 2 p b - 1 2 p b ' - 1 ' with p being vectors of allele frequencies at n markers in populations b and b ' . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; FST differentiation coefficients; segregation variance; and Nei's genetic distance) can be obtained from elements of matrix Γ .

Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome.

In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.

Mapping and functional characterization of structural variation in 1060 pig genomes.

BACKGROUND: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. RESULTS: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies. CONCLUSIONS: This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents.

BACKGROUND: Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. RESULTS: We identified varying numbers (17,497-17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 "missing" genes in birds in general, and 36 of the 174 "missing" genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. CONCLUSION: The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.

Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria.

BACKGROUND: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. RESULTS: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. CONCLUSIONS: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

Whole-genome sequences restore the original classification of dabbling ducks (genus Anas).

Anas, is a genus of dabbling ducks and encompasses a considerable number of species, among which some are the progenitors of domestic ducks. However, the taxonomic position of the Anas genus remains uncertain because several of its species, initially categorized as Anas based on morphological characteristics, were subsequently reclassified and grouped with the South American genus Tachyeres, primarily based on analysis of their mitochondrial gene sequences. Here, we constructed a phylogenetic tree using nine of our recently assembled Anas genomes, two Tachyeres genomes, and one Cairina genome that are publicly available. The results showed that the Northern shoveler (Anas clypeata) and Baikal teal (Anas formosa) clustered with the other Anas species at the whole-genome level rather than with the Steamer ducks (genus Tachyeres). Therefore, we propose to restore the original classification of the Anas genus, which includes the Northern shoveler and Baikal teal species, 47 species in total. Moreover, our study unveiled extensive incomplete lineage sorting and an ancient introgression event from Tachyeres to Anas, which has led to notable phylogenetic incongruence within the Anas genome. This ancient introgression event not only supports the theory that Anas originated in South America but also that it played a significant role in shaping the evolutionary trajectory of Anas, including the domestic duck.

A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.

BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.

An improved chromosome-level genome assembly and annotation of Echeneis naucrates.

Echeneis naucrates, as known as live sharksucker, is famous for the behavior of attaching to hosts using a highly modified dorsal fin with oval-shaped sucking disc. Here, we generated an improved high-quality chromosome-level genome assembly of E. naucrates using Illumina short reads, PacBio long reads and Hi-C data. Our assembled genome spans 572.85 Mb with a contig N50 of 23.19 Mb and is positioned to 24 pseudo-chromosomes. Additionally, at least one telomere was identified for 23 out of 24 chromosomes. Furthermore, we identified a total of 22,161 protein-coding genes, of which 21,402 genes (96.9%) were annotated successfully with functions. The combination of ab initio predictions and Repbase-based searches revealed that 15.57% of the assembled E. naucrates genome was identified as repetitive sequences. The completeness of the genome assembly and the gene annotation were estimated to be 97.5% and 95.4% with BUSCO analyses. This work enhances the utility of the live sharksucker genome and provides a valuable groundwork for the future study of genomics, biology and adaptive evolution in this species.

Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra.

Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

A chromosome-level genome assembly of an avivorous bat species (Nyctalus aviator).

Currently, three carnivorous bat species, namely Ia io, Nyctalus lasiopterus, and Nyctalus aviator, are known to actively prey on seasonal migratory birds (hereinafter referred to as "avivorous bats"). However, the absence of reference genomes impedes a thorough comprehension of the molecular adaptations of avivorous bat species. Herein, we present the high-quality chromosome-scale reference genome of N. aviator based on PacBio subreads, DNBSEQ short-reads and Hi-C sequencing data. The genome assembly size of N. aviator is 1.77 Gb, with a scaffold N50 of 102 Mb, of which 99.8% assembly was anchored into 21 pseudo-chromosomes. After masking 635.1 Mb repetitive sequences, a total of 19,412 protein-coding genes were identified, of which 99.3% were functionally annotated. The genome assembly and gene prediction reached 96.1% and 96.1% completeness of Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. This chromosome-level reference genome of N. aviator fills a gap in the existing information on the genomes of carnivorous bats, especially avivorous ones, and will be valuable for mechanism of adaptations to dietary niche expansion in bat species.

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

Pacific saury (Cololabis saira) is an important fish in several countries. Notably, the catch of this fish has markedly decreased recently, which might be due to environmental changes, including feeding habitat changes. However, no clear correlation has been observed. Therefore, the physiological basis of Pacific saury in relation to possible environmental factors must be understood. We sequenced the genome of Pacific saury and extracted RNA from nine tissues (brain, eye, gill, anterior/posterior guts, kidney, liver, muscle, and ovary). In 1.09 Gb assembled genome sequences, a total of 26,775 protein-coding genes were predicted, of which 26,241 genes were similar to known genes in a public database. Transcriptome analysis revealed that 24,254 genes were expressed in at least one of the nine tissues, and 7,495 were highly expressed in specific tissues. Based on the similarity of the expression profiles to those of model organisms, the transcriptome obtained was validated to reflect the characteristics of each tissue. Thus, the present genomic and transcriptomic data serve as useful resources for molecular studies on Pacific saury. In particular, we emphasize that the gene expression data, which serve as the tissue expression panel of this species, can be employed in comparative transcriptomics on marine environmental responses.

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

Detection of newly synthesized RNA reveals transcriptional reprogramming during ZGA and a role of Obox3 in totipotency acquisition.

Zygotic genome activation (ZGA) after fertilization enables the maternal-to-zygotic transition. However, the global view of ZGA, particularly at initiation, is incompletely understood. Here, we develop a method to capture and sequence newly synthesized RNA in early mouse embryos, providing a view of transcriptional reprogramming during ZGA. Our data demonstrate that major ZGA gene activation begins earlier than previously thought. Furthermore, we identify a set of genes activated during minor ZGA, the promoters of which show enrichment of the Obox factor motif, and find that Obox3 or Obox5 overexpression in mouse embryonic stem cells activates ZGA genes. Notably, the expression of Obox factors is severely impaired in somatic cell nuclear transfer (SCNT) embryos, and restoration of Obox3 expression corrects the ZGA profile and greatly improves SCNT embryo development. Hence, our study reveals dynamic transcriptional reprogramming during ZGA and underscores the crucial role of Obox3 in facilitating totipotency acquisition.

LKRSDH-dependent histone modifications of insulin-like peptide sites contribute to age-related circadian rhythm changes.

To understand aging impact on the circadian rhythm, we screened for factors influencing circadian changes during aging. Our findings reveal that LKRSDH mutation significantly reduces rhythmicity in aged flies. RNA-seq identifies a significant increase in insulin-like peptides (dilps) in LKRSDH mutants due to the combined effects of H3R17me2 and H3K27me3 on transcription. Genetic evidence suggests that LKRSDH regulates age-related circadian rhythm changes through art4 and dilps. ChIP-seq analyzes whole genome changes in H3R17me2 and H3K27me3 histone modifications in young and old flies with LKRSDH mutation and controls. The results reveal a correlation between H3R17me2 and H3K27me3, underscoring the role of LKRSDH in regulating gene expression and modification levels during aging. Overall, our study demonstrates that LKRSDH-dependent histone modifications at dilps sites contribute to age-related circadian rhythm changes. This data offers insights and a foundational reference for aging research by unveiling the relationship between LKRSDH and H3R17me2/H3K27me3 histone modifications in aging.

A genomic basis of vocal rhythm in birds.

Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome.

In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome.

MPH: fast REML for large-scale genome partitioning of quantitative genetic variation.

MOTIVATION: Genome partitioning of quantitative genetic variation is useful for dissecting the genetic architecture of complex traits. However, existing methods, such as Haseman-Elston regression and linkage disequilibrium score regression, often face limitations when handling extensive farm animal datasets, as demonstrated in this study. RESULTS: To overcome this challenge, we present MPH, a novel software tool designed for efficient genome partitioning analyses using restricted maximum likelihood. The computational efficiency of MPH primarily stems from two key factors: the utilization of stochastic trace estimators and the comprehensive implementation of parallel computation. Evaluations with simulated and real datasets demonstrate that MPH achieves comparable accuracy and significantly enhances convergence, speed, and memory efficiency compared to widely used tools like GCTA and LDAK. These advancements facilitate large-scale, comprehensive analyses of complex genetic architectures in farm animals. AVAILABILITY AND IMPLEMENTATION: The MPH software is available at https://jiang18.github.io/mph/.

Adaptive functions of structural variants in human brain development.

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.