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bioRxiv2022

Three new genome assemblies of blue mussel lineages: North and South European Mytilus edulis and Mediterranean Mytilus galloprovincialis.

The blue mussel species complex (Mytilus edulls) is of particular interest both as model species in population genetics and ecology, but also as an economic resource in many regions. Using 10X genomics pseudo-long reads, I assembled genomes of three closely related blue mussel lineages from the Mytllus species complex in the Northern hemisphere. Given the huge diversity within and between lineages in this complex, the objective was to produce affordable genomic resources for population and evolutionary genomic studies to broaden the coverage of this diverse species complex. I used transcriptome guided corrections and scaffolding on a chromosome scale genome of a close species to reduce the fragmentation of the genomes. The result is a set of partially fragmented genomes of equivalent completeness to already published genomes. Three new draft genomes are added to the fast increasing genomic resources of this complex for the Mediterranean M. galloprovlnclalls, the South-European M. edulls and the the North-European M. edulls.

genomics↗
bioRxiv2022

Haplotype-resolved de novo genome assemblies of four coniferous tree species

Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we optimized the DNA library preparation protocols and employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, and Cunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in C. obtusa to 16.0 Mb in L. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3-95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

genomics↗
bioRxiv2022

Transposable element and host silencing activity in gigantic genomes

Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways -- the piRNA pathway and KRAB-ZFP transcriptional repression -- in the male and female gonads of Ranodon sibiricus, a salamander species with a [~]21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both sexes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 - 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Males have higher TE expression than females, suggesting that they may contribute more to the species high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.

genomics↗
bioRxiv2023

Genomes of the human filarial parasites Mansonella perstans and Mansonella ozzardi

The filarial parasites Mansonella ozzardi and Mansonella perstans, causative agents of mansonellosis, infect hundreds of millions of people worldwide, yet remain among the most understudied of the human filarial pathogens. M. ozzardi is highly prevalent in Latin American countries and Caribbean Islands, while M. perstans is predominantly found in sub-Saharan Africa as well as in a few areas in South America. In addition to the differences in their geographical distribution, the two parasites are transmitted by different insect vectors, as well as exhibit differences in their responses to commonly used anthelminthic drugs. The lack of genome information has hindered investigations into the biology and evolution of Mansonella parasites and understanding the molecular basis of the clinical differences between species. In the current study, high quality genomes of two independent clinical isolates of M. perstans from Cameroon and two M. ozzardi isolates one from Brazil and one from Venezuela are reported. The genomes are approximately 76 Mb in size, encode about 10,000 genes each, and are largely complete based on BUSCO scores of about 90%, similar to other completed filarial genomes. These sequences represent the first genomes from Mansonella parasites and enabled a comparative genomic analysis of the similarities and differences between Mansonella and other filarial parasites. Horizontal DNA transfers (HDT) from mitochondria (nuMTs) as well as transfers from genomes of endosymbiotic Wolbachia bacteria (nuWTs) to the host nuclear genome were identified and analyzed. Sequence comparisons and phylogenetic analysis of known targets of anti-filarial drugs diethylcarbamazine (DEC), ivermectin and mebendazole revealed that all known target genes were present in both species, except for the DEC target encoded by gon-2 gene, which is fragmented in genome assemblies from both M. ozzardi isolates. These new reference genome sequences will provide a valuable resource for further studies on biology, symbiosis, evolution and drug discovery.

genomics↗
bioRxiv2023

Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into genetic variants in candidate genes for disease resistance

Detection of genome-wide genetic variation is one of the primary goals in bovine genomics. Genomes of several cattle breeds have been sequenced so far to understand the genetic variation associated with important phenotypes. Red Chittagong Cattle (RCC) is a locally adopted and disease-resistant indicine cattle breed in Bangladesh. In this study, we describe the first genome sequence of the RCC breed and in silico analyses of identified functional variants. Deep sequencing of a RCC bull genome on the NanoBall sequencing platform generated approximately 110 Gb paired-end data, resulting in 31X of genome coverage. Quality filtering retained 360,711,803 paired-end reads. Of the filtered reads, 99.8% were mapped to the bovine reference genome (ARSUCD1.2). A total of 17. 8 million Single nucleotide variants (SNVs) and 2.1 insertions and deletions (INDELs) were identified in the RCC genome. Ts/Tv ratio was computed and found to be 2.21. In total, 332 4621 variants were novel compared with dbSNP data (NCBI dbSNP bovine build 150). Functional annotation identified 54961 SNVs exonic regions, 63.75% of which were synonymous, whereas 30.42% were non-synonymous changes. The percentage of coding INDELs was 0.25% (Frameshift deletion 0.19% and Frameshift insertion 0.06%). We identified 120 variants in 26 candidates for five diseases-foot and mouth disease (FMD), Mastitis, Parasite, para-tuberculosis, and tick. Of the 120 variants, 50 were non-synonymous / frameshift (NS/FS), while 70 were synonymous/non-frameshift (SS/NFS). The identified catalog of genomic variants in RCC may establish a paradigm for cattle research in Bangladesh by filling the void and providing a database for genome-wide variation for future functional studies in RCC.

genomics↗
bioRxiv2023

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of the S. scovelli genome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set for S. scovelli. By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBIs eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involving S. scovelli.

genomics↗
bioRxiv2023

Genomic insights into greater yam tuber quality traits

Yams are important tubers widely consumed in developing countries in various forms, mainly boiled, pounded and fried. Tuber quality is a key criterion for acceptance by the various actors in the value chain. However, the genetics of yam tuber quality has not yet been comprehensively investigated. Given this lack of knowledge, we used population genomics and candidate gene association approaches to unravel the genetic basis of the three main quality attributes of boiled yam, namely texture, starch content and colour indices. We re-sequenced the whole genome of 127 yam genotypes with different quality attributes, and performed an enrichment of the already available functional genome annotation using comparative genomics. Population genomics analysis highlighted three main genetic groups and 1,053 genes under selection. We focused this work on three known quality trait-related pathways: pectin, starch content and flavonoid biosynthesis, and inventoried in the genome all the structural genes related to those pathways by comparative genomics. We improved the functional annotation of the three pathways with 48% more genes. A total of 18 candidate genes containing genetic variants significantly associated with the target traits were detected, including eight genes that were also found under selection. The texture-related candidate genes were distributed between the pectin and starch pathways. Overall, the use of comparative genomics has allowed the generation of an unprecedented genomic resource. The improved functional annotation of the yam genome is a promising predictive tool for identifying other core genes associated with any trait of interest to meet the growing need and diversified demands for yams.

genomics↗
bioRxiv2023

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibits resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly-fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genomes with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence would contribute to elucidating the population structure of this species and could be a milestone in understanding the molecular mechanisms of the pernicious traits and to developing effective weed control strategies to avoid yield loss in rice production.

genomics↗
bioRxiv2023

The human genome's vocabulary as proposed by the DNA language model GROVER

Large Language Models (LLMs) on natural language have achieved a level of performance that allows the generation of coherent and syntactically correct text. DNA sequence of genomes follows rules similar to natural language, but a distinguishing factor is the absence of a concept analogous to words. We established byte-pair tokenization on the human genome and trained a foundation language model called GROVER ("Genome Rules Obtained Via Extracted Representations") to select the optimal vocabulary with a custom fine-tuning task of next-k-mer prediction. We thus defined a dictionary of words/tokens in the human genome that best carries the information content for DNA language models. Analyzing GROVERs learned representations, we observed that token embeddings primarily encode information related to their frequency, sequence content, and length. Some tokens are almost exclusively localized in repeats, while the vast majority widely distributes over the genome. The model also learns context and lexical ambiguity. Average embeddings of genomic regions relate to functional genomics annotation and thus indicate that GROVER has learned these structures purely from the contextual relationships of tokens. That we can extract functional annotations from the genome, purely based on sequence representation to the trained model, highlights the extent of information content encoded by the sequence. This is supported by fine-tuning tasks on genome biology with questions of promoter identity and protein-DNA binding. GROVER learns sequence context, a sense for grammatical structures and language rules in the genome. This knowledge can be extracted and used to compose a grammar book for the code of life.

genomics↗
bioRxiv2023

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

BackgroundGenomic regions that remain poorly understood, often referred to as the "dark genome," contain a variety of functionally relevant and biologically informative genome 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 investigating the dark genome in silico, focusing on EVEs found within vertebrate genomes. ResultsUsing DIGS on 874 vertebrate species genomes, we uncovered 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 ten 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. ConclusionsWe comprehensively catalogue and analyse EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity and long-term evolution of viruses, and revealing 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.

genomics↗
bioRxiv2023

Improving Hi-C contact matrices using genome graphs

Three-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique, has drastically expanded our comprehension of 3D chromosome structures. The first step of Hi-C analysis pipeline involves mapping sequencing reads from Hi-C to linear reference genomes. However, the linear reference genome does not incorporate genetic variation information, which can lead to incorrect read alignments, especially when analyzing samples with substantial genomic differences from the reference such as cancer samples. Using genome graphs as the reference facilitates more accurate mapping of reads, however, new algorithms are required for inferring linear genomes from Hi-C reads mapped on genome graphs and constructing corresponding Hi-C contact matrices, which is a prerequisite for the subsequent steps of the Hi-C analysis such as identifying topologically associated domains and calling chromatin loops. We introduce the problem of genome sequence inference from Hi-C data mediated by genome graphs. We formalize this problem, show the hardness of solving this problem, and introduce a novel heuristic algorithm specifically tailored to this problem. We provide a theoretical analysis to evaluate the efficacy of our algorithm. Finally, our empirical experiments indicate that the linear genomes inferred from our method lead to the creation of improved Hi-C contact matrices. These enhanced matrices show a reduction in erroneous patterns caused by structural variations and are more effective in accurately capturing the structures of topologically associated domains.

genomics↗
bioRxiv2024

Multiplex generation and single cell analysis of structural variants in a mammalian genome

The functional consequences of structural variants (SVs) in mammalian genomes are challenging to study. This is due to several factors, including: 1) their numerical paucity relative to other forms of standing genetic variation such as single nucleotide variants (SNVs) and short insertions or deletions (indels); 2) the fact that a single SV can involve and potentially impact the function of more than one gene and/or cis regulatory element; and 3) the relative immaturity of methods to generate and map SVs, either randomly or in targeted fashion, in in vitro or in vivo model systems. Towards addressing these challenges, we developed Genome-Shuffle-seq, a straightforward method that enables the multiplex generation and mapping of several major forms of SVs (deletions, inversions, translocations) throughout a mammalian genome. Genome-Shuffle-seq is based on the integration of "shuffle cassettes to the genome, wherein each shuffle cassette contains components that facilitate its site-specific recombination (SSR) with other integrated shuffle cassettes (via Cre-loxP), its mapping to a specific genomic location (via T7-mediated in vitro transcription or IVT), and its identification in single-cell RNA-seq (scRNA-seq) data (via T7-mediated in situ transcription or IST). In this proof-of-concept, we apply Genome-Shuffle-seq to induce and map thousands of genomic SVs in mouse embryonic stem cells (mESCs) in a single experiment. Induced SVs are rapidly depleted from the cellular population over time, possibly due to Cre-mediated toxicity and/or negative selection on the rearrangements themselves. Leveraging T7 IST of barcodes whose positions are already mapped, we further demonstrate that we can efficiently genotype which SVs are present in association with each of many single cell transcriptomes in scRNA-seq data. Finally, preliminary evidence suggests our method may be a powerful means of generating extrachromosomal circular DNAs (ecDNAs). Looking forward, we anticipate that Genome-Shuffle-seq may be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and 3D nuclear architecture. We further anticipate potential uses for in vitro modeling of ecDNAs, as well as in paving the path to a minimal mammalian genome.

genomics↗
bioRxiv2024

TIPP_plastid: A user-friendly tool for de novo assembly of plastid genomes

Plant cells have two major organelles with their own genomes: chloroplasts and mitochondria. While chloroplast genomes tend to be structurally conserved, the mitochondrial genomes of plants, which are much larger than those of animals, are characterized by complex structural variation. We introduce TIPPo, a user-friendly, reference-free assembly tool that uses PacBio high-fidelity (HiFi) long-read data and that does not rely on genomes from related species or nuclear genome information for the assembly of organellar genomes. TIPPo employs a deep learning model for initial read classification and leverages k-mer counting for further refinement, significantly reducing the impact of nuclear insertions of organellar DNA on the assembly process. We used TIPPo to completely assemble a set of 54 complete chloroplast genomes. No other tool was able to completely assemble this set. TIPPo is comparable to PMAT in assembling mitochondrial genomes from most species, but does achieve even higher completeness for some species. We also used the assembled organelle genomes to identify instances of nuclear plastid DNA (NUPTs) and nuclear mitochondrial DNA (NUMTs) insertions. The cumulative length of NUPTs/NUMTs positively correlates with the size of the nuclear genome, suggesting that insertions occur stochastically. NUPTs/NUMTs show predominantly C:G to T:A changes, with the mutated cytosines typically found in CG and CHG contexts, suggesting that degradation of NUPT and NUMT sequences is driven by the known elevated mutation rate of methylated cytosines. siRNA loci are enriched in NUPTs and NUMTs, consistent with the RdDM pathway mediating DNA methylation in these sequences.

genomics↗
bioRxiv2024

Matching Excellence: ONT's Rise to Parity with PacBio in Genome Reconstruction of Non-Model Bacterium with High GC Content

Reconstruction of complete bacterial genomes is a vital aspect of microbial research, as it provides complex information about genetic content, gene ontology, and regulation. It has become a domain of 3rd generation, long-read sequencing platforms, as short-read technologies can deliver mainly fragmented genomes. PacBio platform can provide high-quality complete genomes, yet remains one of the most expensive sequencing strategies. Oxford Nanopore Technology (ONT) offers the advantage of producing the longest reads, being at the same time the most cost-effective option in terms of platform costs, as well as library preparation, and sequencing. However, ONTs error rate, although significantly reduced lately, still holds a certain level of distrust in the scientific community. In recent years, hybrid assembly of Nanopore and Illumina data has been used to solve ONTs issue with error rate and has yielded the best results in terms of genome completeness, quality, and price. However, the latest advancements in Nanopore technology, including new flow cells (R10.4.1), new library preparation chemistry (V14) and duplex-mode, updated basecallers (Dorado v0.4.1), and the realization that sequencing in dark mode results in significantly increased throughput, have had a significant impact on the quality of generated data and, thus, the recovery of complete genomes by ONT sequencing alone. In this study, we compared the data generated by ONT using three sequencing strategies (Native barcoding, RAPID barcoding, and custom-developed: BARSEQ) against PacBio and Illumina (NextSeq) as well as Illumina-ONT hybrid data. For this purpose, we employed three strains of the actinobacteria Propionibacterium freudenreichii, whose genomes have been proven difficult to reconstruct due to high GC content, regions of repeated sequences and massive genome rearrangements. Our data indicate that DNA libraries prepared with the native barcoding kit, sequenced with V14 chemistry on R10.4.1 flow cell, and assembled with Flye resulted in the reconstruction of complete genomes of overall quality highly similar to that of genomes reconstructed with PacBio. The highest level of quality can be achieved by hybrid assembly of data from the Native barcoding kit complemented with data from custom-developed BARSEQ, both sequenced on R10.4.1 flow cell. In conclusion, our results demonstrate that ONT can be used as a cost-effective sequencing strategy, without the need for complementing with other sequencing technologies, for the reconstruction of complete genomes of the highest quality.

genomics↗
bioRxiv2024

Development and Implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for Haemophilus influenzae

2.Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome MLST (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N=14) and high-quality draft H. influenzae genomes (N=2,297). The draft genome dataset was divided into a development (N=921) and a validation dataset (N=1,376). The development dataset was used to identify potential core genes with the validation dataset used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearmans correlation and Ordinary Least Square linear regression tests. Preliminary analyses using the development dataset identified 1,067 core genes, which were refined to 1,037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen. 3. Impact statementDiscriminating H. influenzae variants and evaluating population structure has been challenging and largely unstandardised. To address this, we have developed a cgMLST scheme for H. influenzae. Since an accurate typing approach relies on precise reflection of the underlying population structure, we explored various methods to define the scheme. The core genes included in this scheme were predicted to encode functions in essential biological pathways, such as metabolism and genetic information processing, and could be reliably assembled from short-read sequence data. Single-linkage clustering, based on core genome allelic profiles, showed high congruence to genealogy reconstructed by Maximum-Likelihood (ML) methods from the core genome nucleotide alignment. The cgMLST scheme v1 enables rapid and accurate depiction of high-resolution H. influenzae population structure, and making this scheme accessible via the PubMLST database, ensures that microbiology reference laboratories and public health authorities worldwide can use it for genomic surveillance. 4. Data summaryThe H. influenzae cgMLST scheme is accessible via https://pubmlst.org/organisms/haemophilus-influenzae. The list of isolate IDs available publicly from pubmlst.org is provided in Supplementary File 1. The pipeline for cgMLST scheme development and validation is published at https://www.protocols.io/private/EF6DB7FE429311EEB8630A58A9FEAC02. All in-house R and Python scripts for data processing and analysis are available from https://gitfront.io/r/user-4399403/ZHt8DArALHcY/cgmlst-hinf/.

genomics↗
bioRxiv2024

Highly reduced complementary genomes of dual bacterial symbionts in the mulberry psyllid Anomoneura mori

The genomes of obligately host-restricted bacteria suffer from accumulating mildly deleterious mutations, resulting in a drastic size reduction. Psyllids (Hemiptera) are phloem sap-sucking insects with a specialized organ called the bacteriome, which typically harbors two vertically transmitted bacterial symbionts: the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria) and a secondary symbiont phylogenetically diverse among psyllid lineages. Genomes of several Carsonella lineages were revealed to be drastically reduced (158-174 kb), AT-rich (14.0-17.9% GC), and structurally conserved with similar gene inventories devoted for synthesizing essential amino acids scarce in the phloem sap. However, genomic information for secondary symbionts was limited. Hence, this study analyzed genomes of the bacteriome-associated dual symbionts, Secondary_AM (Gammaproteobacteria) and Carsonella_AM, in the mulberry psyllid Anomoneura mori (Psyllidae). This revealed that the Secondary_AM genome is as small and AT-rich (229,822 bp, 17.3% GC) as those of Carsonella, including Carsonella_AM (169,120 bp, 16.2% GC), implying that Secondary_AM is an evolutionarily ancient obligate mutualist like Carsonella. Phylogenomic analyses demonstrated that Secondary_AM is sister to "Candidatus Psyllophila symbiotica" of Cacopsylla spp. (Psyllidae), whose genomes (221-237 kb, 17.3-18.6% GC) were recently reported. The Secondary_AM and Psyllophila genomes showed highly conserved synteny, sharing all genes for complementing the incomplete tryptophan biosynthetic pathway of Carsonella and genes for synthesizing B vitamins. However, sulfur assimilation and carotenoid synthesizing genes were retained only in Secondary_AM and Psyllophila, respectively, indicating ongoing gene silencing. Average nucleotide identity, gene ortholog similarity, genome-wide synteny, and substitution rates suggested that the Secondary_AM/Psyllophila genomes are more labile than the Carsonella genomes.

genomics↗
bioRxiv2024

Genome assembly and annotation of the red flour beetle (Tribolium castaneum) from India

The largest insect order, Coleoptera, includes several economically important beetles that also serve as major model species for biological research. Perhaps foremost among these is the red flour beetle, a global pest of stored grains and flour whose genome was sequenced in 2008. However, the currently available reference genome (Tcas5.2) is incomplete, fragmented and contains many gaps, and the Y chromosome is not assembled. Here we present inTcas1, an updated genome assembly and annotation of T. castaneum collected from India, assembled using both short and long read sequencing, and annotated using two transcriptome datasets. We report that inTcas1 has fewer gaps, less fragmentation, and many new genes and new isoforms of previously annotated genes. This new resource provides a useful update, comparison, and reference for new beetle genome assemblies. The first Y chromosome assembly for this species also provides critical data to study the evolution of insect sex chromosomes and sex determination systems. SIGNIFICANCEWe present here an improved T. castaneum genome assembly (inTcas1) for beetles sampled from India, including the first Y chromosome of this important pest and laboratory model species. The new genome should facilitate more comprehensive analysis of Coleoptera genome and transcriptome datasets, especially beetle populations from Asia - the previously available genome, Tcas5.2, was assembled using the GA2 strain from USA. The updated genome should also facilitate analyses of genome evolution, including sex determination and sex chromosome dynamics; and the new gene annotations can expand the genetic toolkit for this beetle.

genomics↗
bioRxiv2024

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi M[a]ori (M[a]ori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any except Orcinus orca, more single-copy complete BUSCOs than any except Phocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.

genomics↗