Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

Maternal inheritance of functional centrioles in two parthenogenetic nematodes

Centrioles are the core constituent of centrosomes, microtubule-organizing centers involved in directing mitotic spindle assembly and chromosome segregation in animal cells. In sexually reproducing species, centrioles degenerate during oogenesis and female meiosis is usually acentrosomal. Centrioles are retained during male meiosis and, in most species, are reintroduced with the sperm during fertilization, restoring centriole numbers in embryos. In contrast, the presence, origin, and function of centrioles in parthenogenetic species is unknown. We found that centrioles are maternally inherited in two species of asexual parthenogenetic nematodes and identified two different strategies for maternal inheritance evolved in the two species. In Rhabditophanes diutinus, centrioles organize the poles of the meiotic spindle and are inherited by both the polar body and embryo. In Disploscapter pachys, the two pairs of centrioles remain close together and are inherited by the embryo only. Our results suggest that maternally-inherited centrioles organize the embryonic spindle poles and act as a symmetry-breaking cue to induce embryo polarization. Thus, in these parthenogenetic nematodes, centrioles are maternally-inherited and functionally replace their sperm-inherited counterparts in sexually reproducing species.

Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore

As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.

The chromosome-level genomes of the herbal magnoliids Warburgia ugandensis and Saururus chinensis

Warburgia ugandensis and Saururus chinensis are two of the most important medicinal plants in magnoliids and are widely utilized in traditional Kenya and Chinese medicine, respectively. The absence of higher-quality reference genomes has hindered research on the medicinal compound biosynthesis mechanisms of these plants. We report the chromosome-level genome assemblies of W. ugandensis and S. chinensis, and generated 1.13 Gb and 0.53 Gb genomes from 74 and 27 scaffolds, respectively, using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The scaffold N50 lengths were 82.97 Mb and 48.53 Mb, and the assemblies were anchored to 14 and 11 chromosomes of W. ugandensis and S. chinensis, respectively. In total, 24,739 and 20,561 genes were annotated, and 98.5% and 98% of the BUSCO genes were fully represented, respectively. The chromosome-level genomes of W. ugandensis and S. chinensis will be valuable resources for understanding the genetics of these medicinal plants, studying the evolution of magnoliids and angiosperms and conserving plant genetic resources.

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus Laccaria trichodermophora. By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from L. trichodermophora fruit bodies.

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation and prediction when compared to those obtained with short-read technologies, but also allow to understand haplotype divergence. Advances in long-read sequencing technologies in the last years have made it possible to produce such high-quality assemblies for non-model organisms. This allows us to revisit genomes, which have been problematic to scaffold to chromosome-scale with previous generations of data and assembly software. Nematoda, one of the most diverse and speciose animal phyla within metazoans, remains poorly studied, and many previously assembled genomes are fragmented. Using long reads obtained with Nanopore R10.4.1 and PacBio HiFi, we generated highly contiguous assemblies of a diploid nematode of the Mermithidae family, for which no closely related genomes are available to date, as well as a collapsed assembly and a phased assembly for a triploid nematode from the Panagrolaimidae family. Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions.

High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.

The genome of a globally invasive passerine, the common myna, Acridotheres tristis

In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.

First Contiguous Genome Assembly of Japanese Lady Bell (Adenophora triphylla) and Insights into Development of Different Leaf Types

Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination even within the same species. Despite this, few studies have comprehensively characterized the development processes of different leaf types and triterpenoid saponin pathways in this plant. Herein, we provide the first report of a high-quality genome assembly of A. triphylla based on a combination of Oxford Nanopore Technologies and Illumina sequencing methods. Its genome size was estimated to be 2.6 Gb, and the assembled genome finalized as 2.48 Gb, containing 57,729 protein-coding genes. Genome completeness was assessed as 95.6% using the Benchmarking Universal Single-Copy Orthologs score. The evolutionary divergence of A. triphylla was investigated using the genomes of five plant species, including two other species in the Campanulaceae family. The species A. triphylla diverged approximately 51-118 million years ago from the other four plants, and 579 expanded/contracted gene families were clustered in the Gene Ontology terms. The expansion of the β-amyrin synthase (bAS) gene, a key enzyme in the triterpenoid saponin pathway, was identified in the A. triphylla genome. Furthermore, transcriptome analysis of the two leaf types revealed differences in the activity of starch, sucrose, unsaturated fatty acid pathways, and oxidoreductase enzymes. The heat and endoplasmic reticulum pathways related to plant stress were active in the development of round type leaf, while an enhancement of pyrimidine metabolism related to cell development was confirmed in the development of the linear type leaf. This study provides insight into the evolution of bAS genes and the development of different leaf types in A. triphylla.

Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis

Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade.

Mabs, a suite of tools for gene-informed genome assembly

BACKGROUND

Despite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic duplications", which may manifest themselves as cases of alleles being mistakenly assembled as paralogues. Haplotypic duplications are dangerous because they create illusions of gene family expansions and, thus, may lead scientists to incorrect conclusions about genome evolution and functioning.

RESULTS

Here, I present Mabs, a suite of tools that serve as parameter optimizers of the popular genome assemblers Hifiasm and Flye. By optimizing the parameters of Hifiasm and Flye, Mabs tries to create genome assemblies with the genes assembled as accurately as possible. Tests on 6 eukaryotic genomes showed that in 6 out of 6 cases, Mabs created assemblies with more accurately assembled genes than those generated by Hifiasm and Flye when they were run with default parameters. When assemblies of Mabs, Hifiasm and Flye were postprocessed by a popular tool for haplotypic duplication removal, Purge_dups, genes were better assembled by Mabs in 5 out of 6 cases.

CONCLUSIONS

Mabs is useful for making high-quality genome assemblies. It is available at https://github.com/shelkmike/Mabs.

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.

Genomic signatures of disease resistance in endangered staghorn corals

White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.

A practical assembly guideline for genomes with various levels of heterozygosity

Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.

From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.

The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization

Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO₂), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO₂ deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.

Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae)

A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.

The Chromosome-Level Genome of Hestina assimilis (Lepidoptera: Nymphalidae) Reveals the Evolution of Saprophagy-Related Genes in Brush-Footed Butterflies

Most butterflies feed on nectar, while some saprophagous butterflies forage on various non-nectar foods. To date, little is known about the genomic and molecular shifts associated with the evolution of the saprophagous feeding strategy. Here, we assembled the high-quality chromosome-level genome of Hestina assimilis to explore its saprophagous molecular and genetic mechanisms. This chromosome-level genome of H. assimilis is 412.82 Mb, with a scaffold N50 of 15.70 Mb. In total, 98.11% of contigs were anchored to 30 chromosomes. Compared with H. assimilis and other Nymphalidae butterflies, the genes of metabolism and detoxification experienced expansions. We annotated 80 cytochrome P450 (CYP) genes in the H. assimilis genome, among which genes belonging to the CYP4 subfamily were significantly expanded (p < 0.01). These P450 genes were unevenly distributed and mainly concentrated on chromosomes 6-9. We identified 33 olfactory receptor (OR), 20 odorant-binding protein (OBP), and six gustatory receptor (GR) genes in the H. assimilis genome, which were fewer than in the nectarivorous Danaus plexippus. A decreased number of OBP, OR, and GR genes implied that H. assimilis should resort less to olfaction and gustation than their nectarivorous counterparts, which need highly specialized olfactory and gustatory functions. Moreover, we found one site under positive selection occurred in residue 996 (phenylalanine) of GR genes exclusive to H. assimilis, which is conservative in most lineages. Our study provides support for the adaptive evolution of feeding habits in butterflies.

The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments

How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.

Insights from the genomes of 4 diploid Camelina spp

Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant's genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with 3 unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for 4 diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora, and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.

The First Telomere-to-Telomere Chromosome-Level Genome Assembly of Stagonospora tainanensis Causing Sugarcane Leaf Blight

The sexual morph Leptosphaeria taiwanensis Yen and Chi and its asexual morph Stagonospora tainanensis W. H. Hsieh is an important necrotrophic fungal phytopathogen, which causes sugarcane leaf blight, resulting in loss of cane tonnage and sucrose in susceptible sugarcane varieties. Decoding the genome and understanding of the basis of virulence is vitally important for devising effective disease control strategies. Here, we present a 38.25-Mb high-quality genome assembly of S. tainanensis strain StFZ01, denovo assembled with 10.19 Gb Nanopore sequencing long reads (~267×) and 3.82 Gb Illumina short reads (~100×). The genome assembly consists of 12 contigs with N50 of 2.86 Mb of which 5 belong to the telomere to telomere (T2T) chromosome. It contains 13.20% repeat sequences, 12,543 proteins, and 12,206 protein-coding genes with the BUSCO completeness 99.18% at fungi (n = 758) and 99.87% at ascomycota (n = 1706), indicating the high accuracy and completeness of our gene annotations. The virulence analysis in silico revealed the presence of 2379 PHIs, 599 CAZys, 248 membrane transport proteins, 191 cytochrome P450 enzymes, 609 putative secreted proteins, and 333 effectors in the StFZ01 genome. The genomic resources presented here will not only be helpful for development of specific molecular marker and diagnosis technique, population genetics, molecular taxonomy, and disease managements, it can also provide a significant precise genomic reference for investigating the ascomycetous genome, the necrotrophic lifestyle, and pathogenicity in the future.

Genome assembly of Luehdorfia taibai, an endangered butterfly endemic to Qinling Moutains in China with extremely small populations

Conservation genomic resources over the past decade has drastically improved, since genomes can be used to predict diverse parameters vital to conservation management. Luehdorfia taibai is an endemic butterfly only found in restricted aeras in middle-west China and is critically endangered. It was classfied as a vunerlable (VN) species in the “China species red list.” Here we generated 34.38 Gb of raw DNA sequencing reads and obtained a high-qualified draft genome assembly of L. taibai. The final genome is ~683.3 Mb, with contig N50 size of 10.19 Mb. Further, 98.6% of single-copy orthologous genes have been recovered by BUSCO. An estimated 42.34% of the genome of L. taibai consists of repetitive elements. Combined with gene prediction and transcriptome sequencing, genome annotation produced 15,968 protein-coding genes. Additionally, a nearly 1:1 orthology ratio of syntenic blocks between L. taibai and its closest genome Luehdorfia chinensis suggested that the genome structures have not changed much after speciation. The genome of L. taibai have not undergone a whole genome duplication event. Population dynamics analyses indicates that L. taibai has an extremely low heterozygosity of 0.057%, and its population size has declined dramatically over the past 10 thousand years. Our study describes a draft genome assembly of the L. taibai, the first implication of this species. We consider the globally overexploited of the host plants is not the main reason to threaten L. taibai. The genome will provide advice for the conservation to the economically important Luehdorfia lineage and this specific species.

De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America. From a single individual I used long-read nanopore sequencing to assemble a phased diploid genome of 306 Mb and 60X coverage, with quality assessed by a 97.0% BUSCO score, improving upon other ant assemblies. The mitochondrial genome reveals minor rearrangements from other ants. The reads also allowed assembly of parasitic and symbiont genomes. I include a complete Wolbachia bacterial assembly with a size of 1.2 Mb, as well as a commensal symbiont Blochmannia pennsylvanicus, at 791 kb. DNA methylation and hydroxymethylation were measured at base-pair resolution level from the same reads and confirmed extremely low levels seen in the Formicidae family. There was moderate heterozygosity, with 0.16% of bases being biallelic from the parental haplotypes. Protein prediction yielded 14 415 amino acid sequences with 95.8% BUSCO score and 86% matching to previously known proteins. All assemblies were derived from a single MinION flow cell generating 20 Gb of sequence for a cost of $1047 including consumable reagents. Adding fixed costs for equipment brings the total for an ant-sized genome to less than $5000. All analyses were performed in 1 week on a single desktop computer.

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

BACKGROUND

The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences.

RESULTS

Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves.

CONCLUSIONS

The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.

PacBio sequencing output increased through uniform and directional fivefold concatenation

Advances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600-5,000 bp are currently less efficient. For example, the PacBio Sequel I system yields ~ 100,000-300,000 reads with an accuracy per base pair of 90-99%. We sought to sequence several DNA populations of ~ 870 bp in length with a sequencing accuracy of 99% and to the greatest depth possible. We optimised a simple, robust method to concatenate genes of ~ 870 bp five times and then sequenced the resulting DNA of ~ 5,000 bp by PacBioSMRT long-read sequencing. Our method improved upon previously published concatenation attempts, leading to a greater sequencing depth, high-quality reads and limited sample preparation at little expense. We applied this efficient concatenation protocol to sequence nine DNA populations from a protein engineering study. The improved method is accompanied by a simple and user-friendly analysis pipeline, DeCatCounter, to sequence medium-length sequences efficiently at one-fifth of the cost.

A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species

The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around the world. Tea tree has been cultivated and bred in Australia since the 1990s. It has been extensively studied for the genetics and biochemistry of terpene biosynthesis. Here, we report a high quality de novo genome assembly using Pacific Biosciences and Illumina sequencing. The genome was assembled into 3128 scaffolds with a total length of 362 Mb (N50  = 1.9 Mb), with significantly higher contiguity than a previous assembly (N50  = 8.7 Kb). Using a homology-based, RNA-seq evidence-based and ab initio prediction approach, 37,226 protein-coding genes were predicted. Genome assembly and annotation exhibited high completeness scores of 98.1% and 89.4%, respectively. Sequence contiguity was sufficient to reveal extensive gene order conservation and chromosomal rearrangements in alignments with Eucalyptus grandis and Corymbia citriodora genomes. This new genome advances currently available resources to investigate the genome structure and gene family evolution of M. alternifolia. It will enable further comparative genomic studies in Myrtaceae to elucidate the genetic foundations of economically valuable traits in this crop.

Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species

Coleoptera is the most species-rich insect order, yet is currently underrepresented in genomic databases. An assembly was generated for ca. 1.7 Gb genome of the leaf beetle Gonioctena quinquepunctata by first assembling long-sequence reads (Oxford Nanopore; ± 27-fold coverage) and subsequently polishing the resulting assembly with short sequence reads (Illumina; ± 85-fold coverage). The unusually large size (most Coleoptera species are associated with a reported size below 1 Gb) was at least partially attributed to the presence of a large fraction of repeated elements (73.8%). The final assembly was characterized by an N50 length of 432 kb and a BUSCO score of 95.5%. The heterozygosity rate was ± 0.6%. Automated genome annotation informed by RNA-Seq resulted in 40,568 predicted proteins, which is much larger than the typical range 17,000–23,000 predicted for other Coleoptera. However, no evidence of a genome duplication was detected. This new reference genome will contribute to our understanding of genetic variation in the Coleoptera. Among others, it will also allow exploring reproductive barriers between species, investigating introgression in the nuclear genome, and identifying genes involved in resistance to extreme climate conditions.