Complete Genome Assembly Research Articles

Genome-Wide Analysis of the AP2/ERF Family in Oily Persimmon (Diospyros oleifera) and Their Preliminary Roles Exploration in Response to Polyamines for Adventitious Root Formation in Cultivated Persimmon (D. kaki)

The AP2/ERF (APETALA2/Ethylene−Responsive element binding factor) family genes play crucial roles in plant growth and development, and responses to environmental factors; however, this family has not been characterized in Diospyros species. In Diospyros, the diploid Oily persimmon (D. oleifera, 2n = 2x = 30) has been released with complete genome assembly, which makes it possible for genome-wide gene family identification and exploration of molecular function in cultivated persimmon (D. kaki, 2n = 6x = 90). Here, we identified the AP2/ERF family in Oily persimmon for the first time and investigated its classification, main physicochemical properties, structural characteristic, chromosome distribution, gene replication and collinearity, cis-factor binding sites deduction, GO term annotation, and PPI interaction, as well as its expression profiles in different tissue and under the treatment of polyamines. A total of 157 AP2/ERF genes, including four subfamilies (AP2, RAV, Soloist, and ERF), were identified with distribution on all 15 chromosomes. DkAP2/ERF gene expression patterns were extensive and diverse. They were detected expression in every examined tissue, with the highest number of DkAP2/ERF genes expressed in the root. DkAP2/ERF gene expression analysis in adventitious root generation and elongation of polyamines showed their different responses to the action of polyamines, and more pairs of DkAP2/ERF genes with high correlation in gene expression were obtained. In addition, some DkAP2/ERF genes were detected remarkably correlated with genes related to polyamine synthesis and cell metabolism, including S-adenosyl-L-methionine Decarboxyla2 (SAMDC2), D-type cyclin1 (CYCD1), and D-type cyclin2 (CYCD2) genes,. indicating that DkAP2/ERF genes may play a synergistic role in adventitious root development This study was the first to analyze the AP2/ERF gene comprehensively in Diospyros on a genome−wide scale and will provide insights into the application of adventitious root formation in cultivated persimmon.

The complete genome assemblies of 19 insect pests of worldwide importance to agriculture

There are many insect pests worldwide that damage agricultural crop and reduce yield either by direct feeding or by the transmission of plant diseases. To date, control of pest insects has been achieved largely by applying synthetic insecticides. However, insecticide use can be seriously impacted by legislation that limits their use or by the evolution of resistance in the target pest. Thus, there is a move towards less use of insecticides and increased adoption of integrated pest management strategies using a wide range of non-chemical and chemical control methods. For good pest control there is a need to understand the mode of action and selectivity of insecticides, the life cycles of the pests and their biology and behaviours, all of which can benefit from good quality genome data. Here we present the complete assembled (chromosome level) genomes (incl. mtDNA) of 19 insect pests, Agriotes lineatus (click beetle/wireworm), Aphis gossypii (melon/cotton aphid), Bemisia tabaci (cotton whitefly), Brassicogethes aeneus (pollen beetle), Ceutorhynchus obstrictus (seedpod weevil), Chilo suppressalis (striped rice stem borer), Chrysodeixis includens (soybean looper), Diabrotica balteata (cucumber beetle), Diatraea saccharalis (sugar cane borer), Nezara viridula (green stink bug), Nilaparvata lugens (brown plant hopper), Phaedon cochleariae (mustard beetle), Phyllotreta striolata (striped flea beetle), Psylliodes chrysocephala (cabbage stem flea beetle), Spodoptera exigua (beet army worm), Spodoptera littoralis (cotton leaf worm), Diabrotica virgifera (western corn root worm), Euschistus heros (brown stink bug) and Phyllotreta cruciferae (crucifer flea beetle). For the first 15 of these we also present the annotation of genes encoding potential xenobiotic detoxification enzymes. This public resource will aid in the elucidation and monitoring of resistance mechanisms, the development of highly selective chemistry and potential techniques to disrupt behaviour in a way that limits the effect of the pests.

Sipunculus nudus genome provides insights into evolution of spiralian phyla and development

IntroductionSipunculus nudus is the most known species in the genus Sipunculus, distributed in tropical and subtropical coastal waters.MethodsPacBio sequencing and Illumina sequencing were combined for whole-genome sequencing of S. nudus. LC-MS/MS analysis was performed for the metabolomics of S. nudus.ResultsHerein, we report a 1.75 Gb complete genome assembly with a contig N50 size of 450 kb of the S. nudus based on a strategy combining third-generation long-read sequencing and Illumina sequencing. A total of 80391 protein-coding genes are annotated in this genome. Furthermore, gene family evolution analysis shows that S. nudus belonged to Mollusca or was close to Mollusca, but distinct with Annelida. Transcriptome analysis indicates the involvement of complex developmental events in larve. KEGG pathway analysis of differentially expressed genes showed that these DEGs were mainly enriched in the pathway of amino acid metabolism, lipid metabolism and transport and catabolism. LC-MS/MS analysis shows that S. nudus was rich in a variety of nutritional and functional components, such as carnitine, free amino acids, unsaturated fatty acids, inosine and methionine sulfoxide. Combined transcriptome with LC-MS/MS analysis, the results showed that gene expression and metabolic level involved in the inosine, arginine and proline biosynthesis of S. nudus during different growth stages were significantly changed.DiscussionOur genome assembly provides an important genome resource and new insight into the relationships of Sipuncula to other spiralian phyla. Meanwhile, transcriptome and LC-MS/MS analysis reveal the systematic gene expression profiles and metabolite components of S. nudus during different growth stages, which provide new insight into the exploration and development of bioactive molecules of S. nudus.

Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis).

Squamates represent a highly diverse and species-rich vertebrate group that is remarkably understudied from a genomic perspective. A scarcity of genomic data is particularly evident for scincomorph lizards, which encompass over 10% of all living squamates, and for which high-quality genomic resources are currently lacking. To address this knowledge gap, we present the first chromosome-level reference genome for this group, generated from a male Cape cliff lizard (Hemicordylus capensis), using highly accurate PacBio HiFi long-read sequencing data, long-range Omni-C chromosomal conformation capture data and transcriptomic data for annotation. The rHemCap1.1 genome assembly spans 2.29 Gb, with a scaffold N50 of 359.65 Mb, and includes 25,300 protein-coding genes, with a BUSCO completeness score of 95.5% (sauropsida_odb10). We have generated the most contiguous and complete chromosome-level squamate reference genome assembly publicly available to date. Furthermore, we used short-read resequencing of 35 males and females and applied a differential coverage approach to infer the sex-determination system of the species, which was previously unknown. Our results suggest this species has XX/XY sex chromosomes, representing the first evidence of sex determination in the family Cordylidae. This reference genome will help to establish this species as an evolutionary model for studying variation in body armor, a key trait in cordylids and other squamate groups. Lastly, this is the first squamate reference genome from a continental African species and, as such, represents a valuable resource not only for further evolutionary research in cordylids but also in closely related groups.

The gyrfalcon (Falco rusticolus) genome.

High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.

A Nanopore Sequencing Course for Graduate School Curriculum.

The high-throughput long-read sequencing has become affordable enough for any molecular biology lab to utilize genome sequencing in their research. Complete genome sequencing and assembly of bacterial genomes is one such application which is powerful yet simple enough for anyone without advanced molecular biology or bioinformatics skills to conduct on his/her own. High-throughput sequencing will eventually become a basic routine tool in molecular biology labs just like polymerase chain reaction and electrophoresis in a near future. To assist the use of such nanopore sequencing technologies, we designed a graduate school course to learn both the experimental and bioinformatic skills of complete bacterial genome sequencing and assembly.

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.

The phylogenetic signal of structural variation informs a more comprehensive understanding of evolution. As (near-)complete genome assembly becomes more commonplace, the next methodological challenge for inferring genome rearrangement trees is the identification of syntenic blocks of orthologous sequences. In this article, we studied 94 reference quality genomes of primarily Mycobacterium tuberculosis (Mtb) isolates as a benchmark to evaluate these methods. The clonal nature of Mtb evolution, the manageable genome sizes, along with substantial levels of structural variation make this an ideal benchmarking dataset. We tested several methods for detecting homology and obtaining syntenic blocks and two methods for inferring phylogenies from them, then compared the resulting trees to the standard method's tree, inferred from nucleotide substitutions. We found that, not only the choice of methods, but also their parameters can impact results, and that the tree inference method had less impact than the block determination method. Interestingly, a rearrangement tree based on blocks from the Cactus whole-genome aligner was fully compatible with the highly supported branches of the substitution-based tree, enabling the combination of the two into a high-resolution supertree. Overall, our results indicate that accurate trees can be inferred using genome rearrangements, but the choice of the methods for inferring homology requires care. Analysis scripts and code written for this study are available at https://gitlab.com/LPCDRP/rearrangement-homology.pub and https://gitlab.com/LPCDRP/syntement. Supplementary data are available at Bioinformatics online.

Complete genome sequence of Limosilactobacillus fermentum JNU532 as a probiotic candidate for the functional food and feed supplements

Lactic acid bacteria (LAB) have been reported to possess various beneficial properties and are commonly used as probiotics. LAB play a crucial role in milk fermentation, industrial lactic acid fermentation, and health and medicine. Limosilactobacillus fermentum isolated from fermented dairy and food products is considered as 'Generally Recognized as Safe' by FDA. Limosilactobacillus fermentum plays an important role in modulation of the intestinal microbiota, enhancing the host immune system and improving feed digestibility. We isolated a probiotic candidate that was identified and named Limosilactobacillus fermentum JNU532. In a previous report, cell-free culture of L. fermentum JNU532 exhibited anti-melanogenic and antioxidant activities. In this study, we present the complete genome assembly of the bacterial strain JNU532. The final genome consists of one circular chromosome (2,077,416 base pairs) with a guanine + cytosine (GC) ratio of 51.5%.

Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes

Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.

RNA viruses tend to mutate constantly. While many of the variants are neutral, some can lead to higher transmissibility or virulence. Accurate assembly of complete viral genomes enables the identification of underlying variants, which are essential for studying virus evolution and elucidating the relationship between genotypes and virus properties. Recently, third-generation sequencing platforms such as Nanopore sequencers have been used for real-time virus sequencing for Ebola, Zika, coronavirus disease 2019, etc. However, their high per-base error rate prevents the accurate reconstruction of the viral genome. In this work, we introduce a new tool, AccuVIR, for viral genome assembly and polishing using error-prone long reads. It can better distinguish sequencing errors from true variants based on the key observation that sequencing errors can disrupt the gene structures of viruses, which usually have a high density of coding regions. Our experimental results on both simulated and real third-generation sequencing data demonstrated its superior performance on generating more accurate viral genomes than generic assembly or polish tools. The source code and the documentation of AccuVIR are available at https://github.com/rainyrubyzhou/AccuVIR. Supplementary data are available at Bioinformatics online.

1190. Effect of Pulsed Xenon Ultraviolet Light (PX-UV) on Clonal Recovery of Escherichia coli in a Prospective, Sham-controlled, Double-blinded, Interventional, Crossover Trial Conducted in Two Detroit Hospitals

Abstract Background Healthcare-associated infections (HAIs) can be caused by some multidrug-resistant Escherichia coli, most commonly due to production of an extended spectrum beta-lactamase (ESBL), and lead to increased morbidity and mortality. Pulsed Xenon Ultraviolet light (PX-UV), in combination with terminal cleaning, has been shown to improve disinfection and has the potential to lower HAIs by reducing the horizontal spread of infections in hospitals. Here, we assess the effect of PX-UV on the clonal recovery pattern of several E. coli sequence types (STs) using Whole Genome Sequencing (WGS). Methods A prospective, sham-controlled, double-blinded, interventional, crossover trial was conducted to compare standard terminal cleaning with PX-UV (intervention, Group Q) and standard terminal cleaning with sham UV (control, Group W) in 2 Detroit hospitals from 2017 to 2020. Treatments lasted 12 months before crossover, with a 6-month washout period in between (Group R) during which UV was not used. A total of 67 E. coli samples were collected. WGS of the isolates was performed using the Nextseq 550 (Illumina). After de novo assembly, BioNumerics calculation engine (v7.6) was used to complete Whole Genome Multilocus Sequence Type (wgMLST) analysis, assembly free and assembly-based call, and construction of minimum spanning tree (MST). Results The total number of different STs found for the intervention UV device group (Q) and the sham UV device group (W) was 6 while the washout group (R) was 5. Out of the 9 total STs obtained, the most common was ST131 (Table 1). In Group Q, 11 of ST131 were found; 15 were found in Group W. During the washout period (R) 17 of ST131 were found. All other STs had 3 or less circulating clusters. After UV treatment ST1193, ST399, and ST7394 were not recovered. Fig. 1:Minimum spanning tree (MST) for E. coliTable 1:Total number of each sequence type (ST) per treatment group Conclusion During UV intervention 3 different STs (ST1193, ST399, ST7394) were not recovered, but there were negligible changes to the frequency of recovery of the other 6 STs as compared to sham UV treatment. ST131 was the dominant E. coli ST found in Detroit, which is consistent with previously published data stating ST131 as the predominant strain. While PX-UV has previously demonstrated effectiveness on decreasing bioburden, our data does not indicate any remarkable change in clonality and prevalence of E. coli STs after PX-UV use. Disclosures Piyali Chatterjee, PhD, AHRQ Grant # 1R03HS027667-01: Grant/Research Support|AHRQ Grant # 1R03HS027667-01: Central Texas Veterans Health Care System Keith S. Kaye, MD, MPH, Allecra: Advisor/Consultant|GlaxoSmithKline plc.: Receiving symposia honoraria|GlaxoSmithKline plc.: GlaxoSmithKline plc.-sponsored study 212502|Merck: Advisor/Consultant|qpex: Advisor/Consultant|Shionogi: Grant/Research Support|Spero: Advisor/Consultant Chetan Jinadatha, MD, MPH, AHRQ R01 Grant-5R01HS025598: Grant/Research Support|EOS Surfaces: Copper Coupons and materials for testing.

Genome Resource for Acinetobacter schindleri H4-3-C1: An Endophyte of Pseudostellaria heterophylla with Degradation Activity to Toxins Produced by Fungal Pathogens

Acinetobacter schindleri is an endophyte of Pseudostellaria heterophylla, a traditional Chinese herbal plant. It has high degradation activity to toxins produced by fungal pathogen Fusarium graminearum. Here, we deployed PacBio single-molecule real-time long-read sequencing technology to generate a complete genome assembly for the Acinetobacter schindleri H4-3-C1 strain and obtained 1.59 Gb of clean reads. These reads were assembled to a single circular DNA chromosome with a length of 3,265,024 bp, and no plasmid was found in the genome. Totals of 3,193 coding sequences, 91 transfer RNA, 21 ribosomal RNA, and 75 small RNAs were identified in the genome. This high-quality genome assembly and gene annotation resource will facilitate the excavation of the zearalenone degradation gene and provide valuable resources for preventing and controlling toxigenic fungal diseases of P. heterophylla. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Deciphering the mitochondrial genome of Hemerocallis citrina (Asphodelaceae) using a combined assembly and comparative genomic strategy.

Hemerocallis citrina is a perennial herbaceous plant that is dedicated to mothers in Chinese culture and is widely distributed across the country. As a popular species with a long history of cultivation and utilization, it is renowned for its remarkable edible and medicinal value. In this study, we integrated Illumina short-read and Oxford Nanopore long-read sequencing to generate a complete mitochondrial genome (mitogenome) assembly of H. citrina. The H. citrina mitogenome has a multiple chromosomal structure consisting of three circular molecules that are 45,607 bp, 239,991 bp, and 182,864 bp long. We correspondingly annotated 66 genes, comprising 45 protein-coding genes (PCGs), 17 tRNA genes, and 4 rRNA genes. Comparative analysis of gene organization indicated that six syntenic gene clusters were conserved in the mitogenomes of the compared plants. The investigation of repeat content revealed repeat-rich nature of the H. citrina mitogenome, for which plentiful dispersed repeats were characterized to correlate with the size of the mitogenome. The codon usage behavior disclosed that Leucine (Leu) and Serine (Ser) were the most preferred amino acids in H. citrina, and nearly all of the codons with relative synonymous codon usage (RSCU) values greater than 1 showed the preference of A or T ending. Moreover, we inferred a total of 679 RNA editing sites in all mitochondrial PCGs, which presented perfect C-to-U types and tended to lead to the alteration of internal codons. Subsequent selective pressure analysis showed that the majority of the PCGs had undergone evolutionary negative selections, with atp9 in particular undergoing strong stabilizing selection, reflecting its indispensable function in mitogenomes. According to the phylogenetic analysis, H. citrina is close to the species Allium cepa (Amaryllidaceae) and Asparagus officinalis (Asparagaceae) in evolutionary terms. Overall, this project presents the first complete mitogenome of H. citrina, which could provide a reference genome for the comprehensive exploration of the Asphodelaceae family and can facilitate further genomic breeding and evolutionary research on this medicine-food homologous plant.

Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus.

Hydrocephalus, the leading indication for childhood neurosurgery worldwide, is particularly prevalent in low- and middle-income countries. Hydrocephalus preceded by an infection, or postinfectious hydrocephalus, accounts for up to 60% of hydrocephalus in these areas. Since many children with hydrocephalus suffer poor long-term outcomes despite surgical intervention, prevention of hydrocephalus remains paramount. Our previous studies implicated a novel bacterial pathogen, Paenibacillus thiaminolyticus, as a causal agent of neonatal sepsis and postinfectious hydrocephalus in Uganda. Here, we report the isolation of three P. thiaminolyticus strains, Mbale, Mbale2, and Mbale3, from patients with postinfectious hydrocephalus. We constructed complete genome assemblies of the clinical isolates as well as the nonpathogenic P. thiaminolyticus reference strain and performed comparative genomic and proteomic analyses to identify potential virulence factors. All three isolates carry a unique beta-lactamase gene, and two of the three isolates exhibit resistance in culture to the beta-lactam antibiotics penicillin and ampicillin. In addition, a cluster of genes carried on a mobile genetic element that encodes a putative type IV pilus operon is present in all three clinical isolates but absent in the reference strain. CRISPR-mediated deletion of the gene cluster substantially reduced the virulence of the Mbale strain in mice. Comparative proteogenomic analysis identified various additional potential virulence factors likely acquired on mobile genetic elements in the virulent strains. These results provide insight into the emergence of virulence in P. thiaminolyticus and suggest avenues for the diagnosis and treatment of this novel bacterial pathogen. IMPORTANCE Postinfectious hydrocephalus, a devastating sequela of neonatal infection, is associated with increased childhood mortality and morbidity. A novel bacterial pathogen, Paenibacillus thiaminolyticus, is highly associated with postinfectious hydrocephalus in an African cohort. Whole-genome sequencing, RNA sequencing, and proteomics of clinical isolates and a reference strain in combination with CRISPR editing identified type IV pili as a critical virulence factor for P. thiaminolyticus infection. Acquisition of a type IV pilus-encoding mobile genetic element critically contributed to converting a nonpathogenic strain of P. thiaminolyticus into a pathogen capable of causing devastating diseases. Given the widespread presence of type IV pilus in pathogens, the presence of the type IV pilus operon could serve as a diagnostic and therapeutic target in P. thiaminolyticus and related bacteria.

Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades

Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a Marasmius oreades fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.

Complete chloroplast genome sequence of Hibiscus trionum Linnaeus 1753 (Malvaceae)

Hibiscus trionum L. is an annual herbaceous plant belonging to the Malvaceae family. It is native to Central Africa, however, is now naturalized in Europe and Asia including Korea. Here, we report the complete chloroplast genome assembly of H. trionum. The complete chloroplast genome comprises 160,530 bp and is divided into four typical regions: a large single-copy region of 89,272 bp, a pair of inverse repeats of 26,152 bp each, and a small single-copy region of 18,954 bp. A total of 131 genes were identified in this chloroplast, of which 86 were protein-coding, 37 were tRNA, and 8 were rRNA genes. The results of this study will serve as a key reference for further research on Hibiscus speciation.

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families.

Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap.

Recent advancements in long-read sequencing have enabled the telomere-to-telomere (complete) assembly of a human genome and are now contributing to the haplotype-resolved complete assemblies of multiple human genomes. Because the accuracy of read mapping tools deteriorates in highly repetitive regions, there is a need to develop accurate, error-exposing (detecting potential assembly errors), and diploid-aware (distinguishing different haplotypes) tools for read mapping in complete assemblies. We describe the first accurate, error-exposing, and partially diploid-aware VerityMap tool for long-read mapping to complete assemblies.

HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota

Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.