Mb In Length Research Articles

De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene (Rychc) derived from Solanum chacoense.

The isolation of disease resistance genes introduced from wild or related cultivated species is essential for understanding their mechanisms, spectrum and risk of breakdown. To identify target genes not included in reference genomes, genomic sequences with the target locus must be reconstructed. However, de novo assembly approaches of the entire genome, such as those used for constructing reference genomes, are complicated in higher plants. Moreover, in the autotetraploid potato, the heterozygous regions and repetitive structures located around disease resistance gene clusters fragment the genomes into short contigs, making it challenging to identify resistance genes. In this study, we report that a de novo assembly approach of a target gene-specific homozygous dihaploid developed through haploid induction was suitable for gene isolation in potatoes using the potato virus Y resistance gene Rychc as a model. The assembled contig containing Rychc-linked markers was 3.3 Mb in length and could be joined with gene location information from the fine mapping analysis. Rychc was successfully identified in a repeated island located on the distal end of the long arm of chromosome 9 as a Toll/interleukin-1 receptor-nucleotide-binding site-leucine rich repeat (TIR-NBS-LRR) type resistance gene. This approach will be practical for other gene isolation projects in potatoes.

Giant Viruses as a Source of Novel Enzymes for Biotechnological Application.

The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.

A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting.

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.

Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China

In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.

Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers.

Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'.

The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.

Borgs are giant genetic elements with potential to expand metabolic capacity

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as ‘Borgs’. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

Complete-genome sequence and in vitro probiotic characteristics analysis of Bifidobacterium pseudolongum YY-26

The aim was to isolate a neotype bifidobacteria strain and evaluate its in vitro probiotic potential. Bifidobacterium pseudolongum YY-26 (CGMCC 24310) was isolated from faeces of mice treated with low-molecular-weight hydrolyzed guar gum (GMPS) and identified based on 16S rRNA sequence and genome sequence. Whole-genome sequencing obtained using PacBio's single-molecular and Illumina's paired-end sequencing technology. A genome of 2.1Mb in length, with 1877 predicted protein-coding sequences was obtained. Carbohydrate-Activity enZyme analysis revealed that YY-26 encodes 66 enzymes related to carbohydrate metabolism. Whole genome sequence analysis revealed the typical probiotic characteristics of YY-26, including safety in genetic level and ability to produce beneficial metabolites and extracellular polysaccharides. Ability of extensive carbon source utilization and short-chain fatty acid production was observed with single YY-26 cultivation. Considerable acetic acids and lactic acids were determined in GMPS utilization. YY-26 showed tolerance to simulated gastrointestinal tract and displayed appreciable antioxidant activity of free radical scavenging. B. pseudolongum YY-26 was identified with numerous probiotic-associated genes and its probiotic characteristics were verified in vitro. This study supplemented with limited publicly information regarding the genomes of B. pseudolongum strains and revealed the probiotic potential of YY-26.

Species classification and novel plasmid identifications in Arcobacter cryaerophilus and Arcobacter cryaerophilus-like organisms.

The Arcobacter is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other Epsilonproteobacteria. Arcobacter cryaerophilus (A. cryaerophilus) is a heterogeneous species and little is known about its genomic characterization in China. This study aims to determine the genetic and plasmid features of A. cryaerophilus based on whole-genome sequence (WGS). Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (isDDH) were used for the species classification for 90 initially identified A. cryaerophilus strains. One complete genome and 42 draft genomes were obtained by whole genome sequencing. The genomic characteristics were determined using various bioinformatics software. The genomes of the strains examined were estimated to vary from 1.81 to 2.28 Mb in length, with a G + C content of around 27%. ANI and isDDH results indicated that 90 initially identified A. cryaerophilus strains should be reclassified into four new species (ANI > 96% or isDDH > 70%). Two clades (four subclades) were identified among 90 genomes with the phylogenetic analysis. The phylogenetic tree indicated these 90 genomes exhibited a high intra-species genomic diversity. No clustering was assorted with the host or geographic location among these genomes. Aminoglycoside resistance genes, such as aph(2’’)-Ih, AAC(6’)-Ie-APH(2’’)-Ia, aac(6’)-IIa, ant(6), and streptothricin resistance gene SAT-4 were detected in the chromosomes from a third of the Chinese strains. Virulence-related genes were identified in all the sequenced strains. A novel large multiple drug-resistant plasmid (named pCNAC48 with 161,992 bp in length) was identified in strain ICDCAC48. Two antibiotic-resistance islands were found in the plasmid with lengths of 7,950 and 25,137 bp and G + C content of 38.23 and 32.39%, respectively. The drug resistance genes and some transposable elements were cross-distributed among the islands in the plasmid. Antimicrobial susceptibility tests indicated these resistance genes in the plasmid were functional. Plasmid conjugation and curing experiments proved pCNAC48 was stable in strain ICDCAC48. It was the first identified multiple drug resistance plasmid in A. cryaerophilus-like.

Identification of candidate sex-specific genomic regions in male and female Asian arowana genomes.

BackgroundAsian arowana, Scleropages formosus, is one of the most expensive aquarium fish species worldwide. Its sex, however, cannot be distinguished clearly at any development stage, which impedes captive breeding and species protection for this endangered aquarium fish.ResultsTo discover molecular clues to the sex of Asian arowana, we sequenced 26.5 Gb of PacBio HiFi reads and 179.2 Gb of Hi-C reads for 1 male fish and also sequenced 106.5 Gb of Illumina reads, 36.0 Gb of PacBio Sequel reads, and 80.7 Gb of Hi-C reads for 1 female individual. The final male and female genome assemblies were approximately 756.8 Mb and 781.5 Mb in length and contained 25,262 and 25,328 protein-coding genes, respectively. We also resequenced the genomes of 15 male and 15 female individuals with approximately 722.1 Gb of Illumina reads. A genome-wide association study identified several potentially divergent regions between male and female individuals. In these regions, cd48 and cfap52 could be candidate genes for sex determination of Asian arowana. We also found some structural variations in few chromosomes between male and female individuals.ConclusionWe provided an improved reference genome assembly of female arowana and generated the first sequenced genome of 1 male individual. These valuable genetic resources and resequencing data may improve global aquarium fish research.

Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker.

Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (N e ), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current N e of Gauteng was the lowest at 371 animals, while the historical N e across populations suggests that the ancestor N e has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (F ROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high N e and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.

Highly Contiguous Genome Assemblies of the Guinea Paper Wasp (Polistes exclamans) and Mischocyttarus mexicanus.

Paper wasps are a model system for the study of social evolution due to a high degree of inter- and intraspecific variation in cooperation, aggression, and visual signals of social status. Increasing the taxonomic coverage of genomic resources for this diverse clade will aid comparative genomic approaches for testing predictions about the molecular basis of social evolution. Here, we provide draft genome assemblies for two well-studied species of paper wasps, Polistes exclamans and Mischocyttarus mexicanus. The P. exclamans genome assembly is 221.5 Mb in length with a scaffold N50 of 4.11 Mb. The M. mexicanus genome assembly is 227 Mb in length with a scaffold N50 of 1.1 Mb. Genomes have low repeat content (9.54–10.75%) and low GC content (32.06–32.4%), typical of other social hymenopteran genomes. The DNA methyltransferase gene, Dnmt3 , was lost early in the evolution of Polistinae. We identified a second independent loss of Dnmt3 within hornets (genus: Vespa).

A Chromosome-Level Genome Assembly of Toona ciliata (Meliaceae).

Toona ciliata Roem is an important timber species in the Toona genus of the Meliaceae family and an endangered species due to over-cutting and a low rate of natural regeneration in China. Although molecular markers have been applied to studying population genetic diversity, the absence of a reliable reference genome limits in-depth genetic conservation and evolutionary studies of this species. Here, we reported a high-quality assembly of the whole genome sequence of T. ciliata. The total assembled genome has 520.64 Mb in length anchored on 28 chromosomes (contig N50 = 4.48 Mb). A total of 42,159 genes were predicted after the ab initio, homology-based, and transcriptome analyses. A total of 41,284 protein-encoding genes (97.92%) were functionally annotated and 1,246 non-coding RNAs were identified in the T. ciliata genome. Phylogenomic analysis showed that T. ciliata was divergent at 15.06 (6–25) Ma from T. sinensis of the same genus Toona. This whole genome sequence provides a valuable resource to study the genetic conservation and molecular evolution of T. ciliata in the future.

Thalassococcus arenae sp. nov. isolated from sea sand.

A Gram-negative, aerobic, rod-shaped bacterium, designated strain CAU 1522T, was isolated from a sea sand sample collected from the Republic of Korea. Optimal growth of strain CAU 1522T ensued at 30°C, pH 7.5, and 1.0% (w/v) NaCl. Strain CAU 1522T was affiliated to the genus Thalassococcus with high similarity to T. lentus KCTC 32084T (97.5%), T. profundi MCCC 1K03253T (96.5%), and T. halodurans JCM 13833T (96.1%) according to phylogenetic analysis based on 16S rRNA gene sequences. The whole genome of strain CAU 1522T was 3.7Mb in length and included 7 contigs and 3599 protein-coding genes, with a G + C content of 65.4mol%. The predominant cellular fatty acids were C18:1 ω6c and/or C18:1 ω7c (summed feature 8), with Q-10 being the sole isoprenoid quinone. The polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphoglycolipid, and an unidentified lipid. These phenotypic, chemotaxonomic, and phylogenetic data support that strain CAU 1522T is a novel Thalassococcus species, for which the name T. arenae sp. nov. is proposed. The type strain is CAU 1522T (= KCTC 72545T = MCCC 1K04064T).

Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates.

Wohlfahrtia magnifica is a pest fly species, invading livestock in many European, African and Asian countries, and causing heavy agroeconomic losses. In the life cycle of this obligatory parasite, adult flies infect the host by depositing the first‐stage larvae into body cavities or open wounds. The feeding larvae cause severe (skin) tissue damage and potentially fatal infections if untreated. Despite serious health detriments and agroeconomic concerns, genomic resources for understanding the biology of W. magnifica have so far been lacking. Here, we present a complete genome assembly from a single adult female W. magnifica using a Low‐DNA Input workflow for PacBio HiFi library preparation. The de novo assembled genome is 753.99 Mb in length, with a scaffold N50 of 5.00 Mb, consisting of 16,718 predicted protein‐encoding genes. Comparative genomic analysis revealed that W. magnifica has the closest phylogenetic relationship to Sarcophaga bullata followed by Lucilia cuprina. Evolutionary analysis of gene families showed expansions of 173 gene families in W. magnifica that were enriched for gene ontology (GO) categories related to immunity, insecticide‐resistance mechanisms, heat stress response and cuticle development. In addition, 45 positively selected genes displaying various functions were identified. This new genomic resource contributes to the evolutionary and comparative analysis of dipterous flies and an in‐depth understanding of many aspects of W. magnifica biology. Furthermore, it will facilitate the development of novel tools for controlling W. magnifica infection in livestock.

Homologous recombination deficiency predicts response to platinum-based neoadjuvant chemotherapy in early-stage triple-negative breast cancer patients: Secondary analysis of the neocart randomized clinical trial.

e12606 Background: We recently performed the NeoCART trial to compare six cycles of docetaxel plus carboplatin (DCb) with four cycles of epirubicin/cyclophosphamide followed by four cycles of docetaxel (EC-D) in the neoadjuvant setting of triple-negative breast cancer (TNBC). The present study assessed the homologous recombination deficiency (HRD) score, stromal tumor-infiltrating lymphocytes (TILs), and Ki67 as predictors of pathological complete response (pCR) in the NeoCART trial cohort. Methods: Participants in the NeoCART trial (NCT03154749) were randomly assigned, at a 1:1 ratio, to an experimental DCb for 6 cycles (DCb group) or an EC for 4 cycles followed by docetaxel for 4 cycles group (EC-D group). Pretherapeutic formalin-fixed, paraffin-embedded tumor tissues were assessed retrospectively for DNA extraction and sequencing. Sequencing was performed using the Illumina HiSeq4000 platform. The HRD score was calculated based on the genome-wide allele-specific copy number result, and it was composed of three parts: 1) loss of heterozygosity (LOH): the number of segments >=15 Mb in length (but not covering the entire chromosome), mCN =0 and tCN > 0; 2) telomeric allelic imbalance (TAI): the number of segments with allelic imbalances (mCN!= tCN - mCN) extending to the telomeric end of a chromosome; 3) large-scale state transitions (LST), the number of chromosomal breaks between adjacent segments of at least 10 Mb, with a distance between them not larger than 3 Mb. Results: The primary and secondary endpoints, including pCR, event-free survival, overall survival, breast-conserving surgery rates, and treatment-related toxicities, were published previously. HRD testing was attempted on baseline FFPE tumor samples for 54 patients in the NeoCART cohort and was successfully completed for 43 patients (79.6%). It was unavailable for 11 patients due to inadequate tissue or the quality filter. Patients with HRD measurable tumors received DCb in 22 cases and EC-D in 21 cases. TP53 (93.0%), PIK3CA (27.9%), PTEN (11.6%), ATRX (9.3%), NF1 (9.3%), PIK3R1 (9.3%) and PKHD1 (9.3%) were the most frequently mutated genes. No significant association between BRCA1/2 mutation status and pCR was observed in the general population or the two treatment arms. Patients in the DCb group who achieved pCR had a higher HRD score (p =0.04), higher stromal TILs (p =0.02), and a higher Ki67 index (p =0.04) than non-pCR patients. RCB 0/1 was associated with higher stromal TILs (P =0.05) and a higher Ki67 index (P =0.008). However, no correlation between HRD score and pCR was observed in the EC-D group. Conclusions: PCR in TNBC patients correlated with a higher HRD score, higher stromal TILs, and a higher Ki67 index on carboplatin-based neoadjuvant chemotherapy regardless of BRCA status. Clinical trial information: NCT03154749.

Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data.

The Asian swamp eel (Monopterus albus) is an excellent model species for studying sex change and chromosome evolution. M. albus is also widely reared in East Asia and South-East Asia because of its great nutritional value. The low fecundity of this species (about 300 eggs per fish) greatly hinders fries production and breeding programs. Interestingly, about 3–5% of the eels could remain as females for 3 years and lay more than 3,000 eggs per fish, which are referred to as non-sex-reversal (NSR) females. Here, we presented a new chromosome-level genome assembly of such NSR females using Illumina, HiFi, and Hi-C sequencing technologies. The new assembly (Mal.V2_NSR) is 838.39 Mb in length, and the N50 of the contigs is 49.8 Mb. Compared with the previous assembly obtained using the continuous long-read sequencing technology (Mal.V1_CLR), we found a remarkable increase of continuity in the new assembly Mal.V2_NSR with a 20-times longer contig N50. Chromosomes 2 and 12 were assembled into a single contig, respectively. Meanwhile, two highly contiguous haplotype assemblies were also obtained, with contig N50 being 14.54 and 12.13 Mb, respectively. BUSCO and Merqury analyses indicate completeness and high accuracy of these three assemblies. A comparative genomic analysis revealed substantial structural variations (SVs) between Mal.V2_NSR and Mal.V1_CLR and two phased haplotype assemblies, as well as whole chromosome fusion events when compared with the zig-zag eel. Additionally, our newly obtained assembly provides a genomic view of sex-related genes and a complete landscape of the MHC genes. Therefore, these high-quality genome assemblies would provide great help for future breeding works of the swamp eel, and it is a valuable new reference for genetic and genomic studies of this species.

Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser.

The hemiparasitic Taxillus chinensis (DC.) Danser is a root-parasitizing medicinal plant with photosynthetic ability, which is lost in other parasitic plants. However, the cultivation and medical application of the species are limited by the recalcitrant seeds of the species, and even though the molecular mechanisms underlying this recalcitrance have been investigated using transcriptomic and proteomic methods, genome resources for T. chinensis have yet to be reported. Accordingly, the aim of the present study was to use nanopore, short-read, and high-throughput chromosome conformation capture sequencing to construct a chromosome-level assembly of the T. chinensis genome. The final genome assembly was 521.90 Mb in length, and 496.43 Mb (95.12%) could be grouped into nine chromosomes with contig and scaffold N50 values of 3.80 and 56.90 Mb, respectively. In addition, a total of 33,894 protein-coding genes were predicted, and gene family clustering identified 11 photosystem-related gene families, thereby indicating photosynthetic ability, which is a characteristic of hemiparasitic plants. This chromosome-level genome assembly of T. chinensis provides a valuable genomic resource for elucidating the genetic basis underlying the recalcitrant characteristics of T. chinensis seeds and the evolution of photosynthesis loss in parasitic plants.

A chromosome-level genome of the human blood fluke Schistosoma japonicum identifies the genomic basis of host-switching.

The evolution and adaptation of S.japonicum, a zoonotic parasite that causes human schistosomiasis, remain unclear because of the lack of whole-genome data. We construct a chromosome-level S.japonicum genome and analyze it together with 72 samples representing six populations of the entire endemic region. We observe a Taiwan zoophilic lineage splitting from zoonotic populations ∼45,000 years ago, consistent with the divergent history of their intermediate hosts. Interestingly, we detect a severe population bottleneck in S.japonicum, largely coinciding with human history in Asia during the last glacial maximum. We identify several genomic regions underlying natural selection, including GATAD2A and Lmln, both showing remarkable differentiation among different areas. RNAi knockdown suggests association of GATAD2A with parasite development and infection in definitive hosts, while Lmln relates to the specificity of the intermediate hosts. Our study provides insights into the evolution of S.japonicum and serves as a resource for further studies.

The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome.

The lesser marbled fritillary, Brenthis ino (Rottemburg, 1775), is a species of Palearctic butterfly. Male Brenthis ino individuals have been reported to have between 12 and 14 pairs of chromosomes, a much-reduced chromosome number than is typical in butterflies. Here, we present a chromosome-level genome assembly for Brenthis ino, as well as gene and transposable element annotations. The assembly is 411.8 Mb in length with a contig N50 of 9.6 Mb and a scaffold N50 of 29.5 Mb. We also show evidence that the male individual from which we generated HiC data was heterozygous for a neo-Z chromosome, consistent with inheriting 14 chromosomes from one parent and 13 from the other. This genome assembly will be a valuable resource for studying chromosome evolution in Lepidoptera, as well as for comparative and population genomics more generally.