Repetitive Genome Research Articles

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.

Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome‐wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS‐based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two‐step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high‐confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high‐quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.

Highly accurate long-read HiFi sequencing data for five complex genomes

The PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.

Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach

Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from 'Viroflay' × 'Cornell-NO. 9' was used for genetic mapping by resequencing genotyping. In the paternal 'Cornell-NO. 9' map, 212,414 SNPs were mapped, and the total linkage distance was 476.83cM; the maternal 'Viroflay' map included 29,282 SNPs with 401.28cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2cM of LG1 in the 'Cornell-NO. 9' map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.

Orientia tsutsugamushi.

Orientia tsutsugamushi is an obligate intracellular bacterial pathogen that causes the mite-borne human disease scrub typhus, one of the most widespread and severe rickettsial infections. Symptoms typically begin 7–14 days after inoculation and include headache, fever, rash, myalgia, and a painless eschar at the site of the mite’s bite. Untreated, the disease can escalate to cause multiple organ failure and death. Major challenges to disease control include slow and inaccurate diagnostic tests and low awareness amongst clinicians. O. tsutsugamushi infects a range of host cell types including endothelial cells, monocytes/macrophages, and dendritic cells, and it replicates directly in the host cell cytoplasm. Aspects of its infection cycle and biology differentiate it from other genera in the family Rickettsiaceae; these include a microtubule-driven mode of motility, a budding mechanism of host cell exit, a minimal peptidoglycan-like cell wall, and a highly repetitive genome. An obligate intracellular bacterium that infects monocytes, macrophages, dendritic cells, and endothelial cells; it disseminates via blood and lymphatic systems. O. tsutsugamushi lives in trombiculid mites. A single circular chromosome of 1.93–2.47 Mb. No known plasmids. 2086–2709 predicted genes, with a core genome of 657 genes. One of the most highly repetitive bacterial genomes known. Almost 50% of the genome is comprised of repetitive DNA elements. No lipopolysaccharides (LPS). Minimal peptidoglycan-like structure in the cell wall. The organism encodes multiple Ankyrin-repeat-containing effector proteins that interact with host cell pathways. The outer membrane is dominated by highly abundant surface protein TSA56. This has variable domains that differ between strains. This protein is important in serological diagnostics and as a vaccine candidate. The doubling time is approximately 8–9 h. Currently, the organism is genetically intractable. Poor natural immunity; reinfections are common. Historically confined to Asia-Pacific but recent reports of locally acquired cases in the Middle East and Latin America. Estimated to infect at least one million people each year globally and likely the most common treatable cause of nonmalarial fever in the Asia-Pacific region. Responsive to doxycycline (primary choice), azithromycin, rifampicin, and chloramphenicol. Serology and molecular techniques are the main diagnostic approaches, but both have important limitations. There is currently no preventative vaccine available. KINGDOM: Bacteria PHYLUM: Proteobacteria CLASS: Alphaproteobacteria ORDER: Rickettsiales FAMILY: Rickettsiaceae GENUS: Orientia SPECIES: tsutsugamushi KEY STRAINS: Karp, Kato, Gilliam, Boryong, Ikeda, TA716, TA763, TA686, Kawasaki, Kuroki, Saitama, Shimokoshi Gram-negative, pleomorphic rod-shaped bacterium

Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review)

Copy number variations (CNVs) are repetitive genome segments, ranging from one thousand to several million base pairs and varying between individuals in a population. Due to a larger genome coverage compared to SNP markers, CNVs are important sources of genetic variation and are currently considered as an alternative type of DNA markers. The identification of CNV regions (CNVRs) which overlap with genes and quantitative trait loci (QTLs) in livestock genomes are of the greatest interest. In the review, the results of studies on CNV in various livestock species, are summarized and analyzed including the identification of candidate genes whose loci overlap with CNV regions. In addition, the methodological approaches for detection of copy number variations are briefly described. The number of identified CNVRs and a genome coverage ratio were 51-1265 and 0.5-20 % in cattle, 565 CNVRs and 5.84 % in pigs, 978 CNVR and 8.96 % in goats, 3488 CNVR and 2.7 % in sheep. Loci of functional candidate genes associated with economically significant traits overlap with CNVR in all livestock species. There were identified genes associated with growth and development indicators (MYH3 and GBP4 in cattle; ANP32B, GYS1 and CAV1 in pigs; MYLK4 in goats; SHE, BAG4, PIGY and ORMDL1 in sheep); affecting the reproductive traits and fertility (PRP1 and PRP6 in goats; PTGS1 in sheep); associated with meat productivity (KDM5B, ADAM8 and SHH in goats); responsible for various coat and skin colour phenotypes (KIT in pigs; ASIP, AHCY and ITCH in sheep and goats) and involved in the regulation of metabolic processes (PPARA, RXRA, ADD1, FASN and PPP1CA in sheep). The analysis of international experience showed that identified CNVs could be proposed as potential candidates for selection according to economically significant traits in livestock.

Pilar Catalán.

Pilar Catalán.

Abstract 1320: The landscape of somatic substitutions in the repetitive genome across cancer types

Abstract Somatic mutation calling from bulk DNA sequencing is a complex problem susceptible to elevated false positive rates. High mapping quality is considered an important feature of reliable variant calls. At the resolution of short reads, ~10% of the genome displays high sequence similarity with at least one other genomic region and is assigned low mapping quality by alignment algorithms. These low-mapping-quality regions represent recurrent blind spots for mutation callers, which discard many of the variants they harbor, overlooking true biological variation. Here, we developed a pipeline to call substitutions in the low-mapping-quality genome. We used a published thesaurus approach to annotate the variant positions with their high-similarity links. We trained a classifier to emulate high-quality consensus calls made in unique regions using 20 features unrelated to mapping quality, reaching ~95% accuracy in those regions. In an independent sample more than 90% of the thesaurus calls were validated through linked-read sequencing. We then applied the classifier to all candidate substitutions of 2,658 cancer whole genomes from the PCAWG/ICGC consortium including variants falling in low-mapability regions. We retrieve hidden thesaurus variants genome-wide in ~6% of the genome, including genic, coding, and promoter regions. Thesaurus calls are directly proportional in numbers to somatic calls falling in the low-mapping-quality genome and share a similar trinucleotide context spectrum. Rescuing these mutations reveal hidden signal in known cancer genes, including PIK3CA, and excess of mutations genome-wide in promoter, untranslated, and coding regions of many other genes. We also find potential excess of non-synonymous mutations, including in genes from the TRIM and POTE families, having been previously implicated in multiple cancer types. Altogether, we developed a pipeline to call somatic substitutions in the low-mapping-quality genome and uncovered hidden somatic changes along the genomes of human cancers. In the future, this pipeline could be extended to indels and structural variants, and applied to the study of de novo germline variants. Citation Format: Maxime Tarabichi, Jonas Demeulemeester, Annelien Verfaillie, Peter Van Loo, Tomasz Konopka. The landscape of somatic substitutions in the repetitive genome across cancer types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1320.

The nuclear and mitochondrial genomes of Frieseomelitta varia \u2013 a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

BackgroundMost of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste.ResultsThe assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication.ConclusionsThe total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.

Oxford Nanopore sequencing: new opportunities for plant genomics?

DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.

We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley.

Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae).

Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.

Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti

BackgroundAedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large and highly repetitive genome of Ae. aegypti makes it difficult to detect inversions with paired-end short-read sequencing data, and polytene chromosome analysis does not provide sufficient resolution to detect chromosome banding patterns indicative of inversions.ResultsTo characterize chromosomal diversity in this species, we have carried out deep Illumina sequencing of linked-read (10X Genomics) libraries in order to discover inversion loci as well as SNPs. We analyzed individuals from colonies representing the geographic limits of each subspecies, one contact zone between subspecies, and a closely related sister species. Despite genome-wide SNP divergence and abundant microinversions, we do not find any inversions occurring as fixed differences between subspecies. Many microinversions are found in regions that have introgressed and have captured genes that could impact behavior, such as a cluster of odorant-binding proteins that may play a role in host feeding preference.ConclusionsOur study shows that inversions are abundant and widely shared among subspecies of Aedes aegypti and that introgression has occurred in regions of secondary contact. This library of 32 novel chromosomal inversions demonstrates the capacity for linked-read sequencing to identify previously intractable genomic rearrangements and provides a foundation for future population genetics studies in this species.

Cytomolecular diversity of the subtribe Laeliinae (Epidendroidae, Orchidaceae) suggests no relationship between genome size and heterochromatin abundance

The subtribe Laeliinae (Orchidaceae) comprises approximately 2000 species and 38 genera, with numerically stable karyotypes of 2n = 40 (x = 20) in most species. Cytomolecular and chromosome banding analyses have not yet been combined with phylogenetic studies, making the understanding of chromosomal evolution in the group more difficult. The present work sought to perform comparative cytogenetic analyses of representatives of the subtribe Laeliinae, followed by the interpretation of that data within an evolutive context. We analyzed 23 species from seven genera for their chromosome numbers and morphology, the distribution of CMA and DAPI bands, fluorescent in situ hybridization (FISH) with 5S and 35S rDNA and DNA quantification by flow cytometry. All of the species showed 2n = 40, suggesting an apparent macrostructural karyotypic stability, except the polyploids Encyclia alboxanthina, E. jenischiana, E. seidelii, Laelia gouldiana and Prosthechea faresiana (2n = 80). At least two CMA+/DAPI− terminal bands were observed in all analyzed species. Additionally, CMA+/DAPI− blocks were observed in the pericentromeric region of species of the genera Brassavola, Cattleya (except C. trianae) and Laelia. Terminal CMA−/DAPI+ bands were observed in representatives of Brassavola, Laelia and Guarianthe. The clade Brassavola + Cattleya + Laelia, that presented high number of heterochromatic bands, also showed expansions of the numbers of 5S rDNA sites. DNA contents varied from 2C = 2.85 pg (Prosthechea fragrans) to 2C = 5.76 pg (Laelia gouldiana) without relation with number of CMA/DAPI bands or 5S rDNA sites. The relationship between the amplification of repetitive DNAs (viewed here as rDNA sites or heterochromatic bands) and genome size variation is discussed and compared with other plant groups.

Improved genomic resources for the black tiger prawn (Penaeus monodon)

World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N50 length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N50 length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.

A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes.

Endogenous viral elements (EVEs) are found in many eukaryotic genomes. Despite considerable knowledge about genomic elements such as transposons (TEs) and retroviruses, we still lack information about nonretroviral EVEs. Aedes aegypti mosquitoes have a highly repetitive genome that is covered with EVEs. Here, we identified 129 nonretroviral EVEs in the AaegL5 version of the A. aegypti genome. These EVEs were significantly associated with TEs and preferentially located in repeat-rich clusters within intergenic regions. Genome-wide transcriptome analysis showed that most EVEs generated transcripts although only around 1.4% were sense RNAs. The majority of EVE transcription was antisense and correlated with the generation of EVE-derived small RNAs. A single genomic cluster of EVEs located in a 143 kb repetitive region in chromosome 2 contributed with 42% of antisense transcription and 45% of small RNAs derived from viral elements. This region was enriched for TE-EVE hybrids organized in the same coding strand. These generated a single long antisense transcript that correlated with the generation of phased primary PIWI-interacting RNAs (piRNAs). The putative promoter of this region had a conserved binding site for the transcription factor Cubitus interruptus, a key regulator of the flamenco locus in Drosophila melanogaster. Here, we have identified a single unidirectional piRNA cluster in the A. aegypti genome that is the major source of EVE transcription fueling the generation of antisense small RNAs in mosquitoes. We propose that this region is a flamenco-like locus in A. aegypti due to its relatedness to the major unidirectional piRNA cluster in Drosophila melanogaster.

DNA Helicases as Safekeepers of Genome Stability in Plants.

Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety of DNA helicases that are required to ensure genome stability in plants. Due to their sessile lifestyle, plants are especially exposed to harmful environmental factors. Moreover, many crop plants have large and highly repetitive genomes, making them absolutely dependent on the correct interplay of DNA helicases for safeguarding their stability. Although basic features of a number of these enzymes are conserved between plants and other eukaryotes, a more detailed analysis shows surprising peculiarities, partly also between different plant species. This is additionally of high relevance for plant breeding as a number of these helicases are also involved in crossover control during meiosis and influence the outcome of different approaches of CRISPR/Cas based plant genome engineering. Thus, gaining knowledge about plant helicases, their interplay, as well as the manipulation of their pathways, possesses the potential for improving agriculture. In the long run, this might even help us cope with the increasing obstacles of climate change threatening food security in completely new ways.

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

BackgroundSequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations.ResultsWe benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species.ConclusionsThe benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

Chromatin Profiling of the Repetitive and Nonrepetitive Genomes of the Human Fungal Pathogen Candida albicans.

Eukaryotic genomes are packaged into chromatin structures that play pivotal roles in regulating all DNA-associated processes. Histone posttranslational modifications modulate chromatin structure and function, leading to rapid regulation of gene expression and genome stability, key steps in environmental adaptation. Candida albicans, a prevalent fungal pathogen in humans, can rapidly adapt and thrive in diverse host niches. The contribution of chromatin to C. albicans biology is largely unexplored. Here, we generated the first comprehensive chromatin profile of histone modifications (histone H3 trimethylated on lysine 4 [H3K4me3], histone H3 acetylated on lysine 9 [H3K9Ac], acetylated lysine 16 on histone H4 [H4K16Ac], and γH2A) across the C. albicans genome and investigated its relationship to gene expression by harnessing genome-wide sequencing approaches. We demonstrated that gene-rich nonrepetitive regions are packaged into canonical euchromatin in association with histone modifications that mirror their transcriptional activity. In contrast, repetitive regions are assembled into distinct chromatin states; subtelomeric regions and the ribosomal DNA (rDNA) locus are assembled into heterochromatin, while major repeat sequences and transposons are packaged in chromatin that bears features of euchromatin and heterochromatin. Genome-wide mapping of γH2A, a marker of genome instability, identified potential recombination-prone genomic loci. Finally, we present the first quantitative chromatin profiling in C. albicans to delineate the role of the chromatin modifiers Sir2 and Set1 in controlling chromatin structure and gene expression. This report presents the first genome-wide chromatin profiling of histone modifications associated with the C. albicans genome. These epigenomic maps provide an invaluable resource to understand the contribution of chromatin to C. albicans biology and identify aspects of C. albicans chromatin organization that differ from that of other yeasts.IMPORTANCE The fungus Candida albicans is an opportunistic pathogen that normally lives on the human body without causing any harm. However, C. albicans is also a dangerous pathogen responsible for millions of infections annually. C. albicans is such a successful pathogen because it can adapt to and thrive in different environments. Chemical modifications of chromatin, the structure that packages DNA into cells, can allow environmental adaptation by regulating gene expression and genome organization. Surprisingly, the contribution of chromatin modification to C. albicans biology is still largely unknown. For the first time, we analyzed C. albicans chromatin modifications on a genome-wide basis. We demonstrate that specific chromatin states are associated with distinct regions of the C. albicans genome and identify the roles of the chromatin modifiers Sir2 and Set1 in shaping C. albicans chromatin and gene expression.

Architecture of Wheat Inflorescence: Insights from Rice.

The inflorescence architecture of grass crops affects the number of kernels and final grain yield. Great progress has been made in genetic analysis of rice inflorescence development in the past decades. However, the advances in wheat largely lag behind those in rice due to the repetitive and polyploid genomes of wheat. In view of the similar branching patterns and developmental characteristics between rice and wheat, the studies on inflorescence architecture in rice will facilitate related studies in wheat in the future. Here, we review the developmental regulation of inflorescences in rice and wheat and highlight several pathways that potentially regulate the inflorescence architecture of wheat.

Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi

Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation, and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ∼16 Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single-copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource because it now constitutes a high-quality assembly available for TcII (clade C), a prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of these parasites and reinforces the idea that T. cruzi is intraspecifically divided in three main clades. Finally, this work represents the introduction of Nanopore technology to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes.