Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

Abstract Background Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. Results Here, we report de novo genome assemblies of Capsicum annuum ‘Early Calwonder (non-pungent, ECW)’ and ‘Small Fruit (pungent, SF)’ along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers. Conclusions Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.

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Genome sequence of the model rice variety KitaakeX

10.1101/653089 ◽

2019 ◽

Author(s):

Rashmi Jain ◽

Jerry Jenkins ◽

Shengqiang Shu ◽

Mawsheng Chern ◽

Joel A. Martin ◽

...

Keyword(s):

Oryza Sativa ◽

Rice Plant ◽

De Novo ◽

Rice Variety ◽

High Quality ◽

Protein Coding ◽

Genomic Variations ◽

Protein Coding Genes ◽

Gene Annotations ◽

High Quality Genome

AbstractHere, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.

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Insights into the Genome Sequence ofChromobacterium amazonenseIsolated from a Tropical Freshwater Lake

International Journal of Genomics ◽

10.1155/2018/1062716 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

Alexandre Bueno Santos ◽

Patrícia Silva Costa ◽

Anderson Oliveira do Carmo ◽

Gabriel da Rocha Fernandes ◽

Larissa Lopes Silva Scholte ◽

...

Keyword(s):

De Novo ◽

Genomic Diversity ◽

Protein Coding ◽

Biotechnological Potential ◽

Draft Assembly ◽

Functional Studies ◽

Alpha Hemolysin ◽

Type Iv ◽

Nudix Hydrolases ◽

Colicin V

Members of the genusChromobacteriumhave been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis ofChromobacterium amazonensestrain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike otherChromobacteriumspecies, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of theC. amazonensestrain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involvingChromobacterium-related isolates and improves our understanding of the global genomic diversity ofChromobacteriumspecies.

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Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study

Molecular Biology and Evolution ◽

10.1093/molbev/msaa109 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2584-2600 ◽

Cited By ~ 3

Author(s):

Bryan D Clifton ◽

Jamie Jimenez ◽

Ashlyn Kimura ◽

Zeinab Chahine ◽

Pablo Librado ◽

...

Keyword(s):

Gene Family ◽

Sequence Similarity ◽

Gene Families ◽

Read Depth ◽

Specific Gene ◽

Protein Variant ◽

Protein Coding ◽

Expression Levels ◽

Number Variation ◽

Reference Quality

Abstract Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3–7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3′ ends, with 3–5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

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Liftoff: accurate mapping of gene annotations

Bioinformatics ◽

10.1093/bioinformatics/btaa1016 ◽

2020 ◽

Author(s):

Alaina Shumate ◽

Steven L Salzberg

Keyword(s):

Reference Genome ◽

Supplementary Information ◽

Closely Related Species ◽

Protein Coding ◽

Human Reference Genome ◽

Sequence Identity ◽

Gene Annotations ◽

Genome Assemblies ◽

Average Sequence Identity ◽

High Quality Genome

Abstract Motivation Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. Results One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity. Availability and Implementation Liftoff can be installed via bioconda and PyPI. Additionally, the source code for Liftoff is available at https://github.com/agshumate/Liftoff Supplementary information Supplementary data are available at Bioinformatics online.

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De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

10.1101/549790 ◽

2019 ◽

Cited By ~ 2

Author(s):

Siuli Mitra ◽

Ara Sreenivas ◽

Divya Tej Sowpati ◽

Amitha Sampat Kumar ◽

Gowri Awasthi ◽

...

Keyword(s):

De Novo ◽

Diversity Index ◽

Conservation Status ◽

Single Copy ◽

Genomic Diversity ◽

Segmental Duplications ◽

Sequence Coverage ◽

Protein Coding ◽

Asiatic Lion ◽

Specific Expansion

AbstractWe report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. Comparative analysis with other felids and mammalian genomes unraveled the evolutionary history of Asiatic lion and its position among other felids. The genome is estimated to be 2.3 Gb (Gigabase) long with 62X sequence coverage and is found to have 20,543 protein-coding genes. About 2.66% of the genome is covered by simple sequence repeats (SSRs) and 0.4% is estimated to have segmental duplications. Comparison with seven well annotated genomes indicates the presence of 6,295 single copy orthologs, 4 co-orthologs, 21 paralogs uniquely present in Asiatic lion and 8,024 other orthologs. Assessment of male and female transcriptomes gave a list of genes specifically expressed in the male.Our genomic analyses provide candidates for phenotypes characteristic to felids and lion, inviting further confirmation of their contribution through population genetic studies. An Asiatic lion-specific expansion is detected in the Cysteine Dioxygenase-I (CDO-I) family that is responsible for taurine biosynthesis in cats. Wilm’s tumor-associated protein (WT1) family, a non-Y chromosome genetic factor underlying male-sex determination and differentiation is found to have undergone expansion, interestingly like that of the human genome. Another protein family, translation machinery-associated protein 7 (TMA7) that has undergone expansion in humans, also expanded in Asiatic lion and can be further investigated as a candidate responsible for mane in lions because of its role in hair follicle morphogenesis.

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Reference Genome for the Highly Transformable Setaria viridis ME034V

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401345 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3467-3478 ◽

Cited By ~ 2

Author(s):

Peter M. Thielen ◽

Amanda L. Pendleton ◽

Robert A. Player ◽

Kenneth V. Bowden ◽

Thomas J. Lawton ◽

...

Keyword(s):

De Novo ◽

Gene Families ◽

Model Organisms ◽

Phylogenomic Analysis ◽

Setaria Viridis ◽

Sequencing Technology ◽

Protein Coding ◽

Genotype Frequencies ◽

Green Foxtail ◽

Genome Assemblies

Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.

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Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

BMC Biology ◽

10.1186/s12915-021-00994-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Raúl A. González-Pech ◽

Timothy G. Stephens ◽

Yibi Chen ◽

Amin R. Mohamed ◽

Yuanyuan Cheng ◽

...

Keyword(s):

De Novo ◽

Gene Families ◽

Specific Gene ◽

Free Living ◽

Microbial Eukaryotes ◽

The Family ◽

Structural Divergence ◽

Genome Features ◽

Genome Divergence ◽

Genome Assemblies

Abstract Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features. Results Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. Conclusions Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.

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Lost in Translation: The Pitfalls of Ensembl Gene Annotations Between Human Genome Assemblies and Their Impact on Diagnostics

10.21203/rs.3.rs-131927/v1 ◽

2020 ◽

Author(s):

Mohammed O.E Abdallah ◽

Mahmoud Koko ◽

Raj Ramesar

Keyword(s):

Human Genome ◽

Genome Assembly ◽

Evolutionary Constraint ◽

Clinical Genetics ◽

Ensembl Gene ◽

Protein Coding ◽

Gene Annotations ◽

Human Genome Assembly ◽

Gene Models ◽

Genome Assemblies

Abstract Background:The GRCh37 human genome assembly is still widely used in genomics despite the fact an updated human genome assembly (GRCh38) has been available for many years. A particular issue with relevant ramifications for clinical genetics currently is the case of the GRCh37 Ensembl gene annotations which has been archived, and thus not updated, since 2013. These Ensembl GRCh37 gene annotations are just as ubiquitous as the former assembly and are the default gene models used and preferred by the majority of genomic projects internationally. In this study, we highlight the issue of genes with discrepant annotations, that have been recognized as protein coding in the new but not the old assembly. These genes are ignored by all genomic resources that still rely on the archived and outdated gene annotations. Moreover, the majority if not all of these discrepant genes (DGs) are automatically discarded and ignored by all variant prioritization tools that rely on the GRCh37 Ensembl gene annotations.Methods:We performed bioinformatics analysis identifying Ensembl genes with discrepant annotations between the two most recent human genome assemblies, hg37, hg38, respectively. Clinical and phenotype gene curations have been obtained and compared for this gene set. Furthermore, matching RefSeq transcripts have also been collated and analyzed. ٌResults:We found hundreds of genes (N=267) that were reclassified as “protein-coding” in the new hg38 assembly. Notably, 169 of these genes also had a discrepant HGNC gene symbol between the two assemblies.Most genes had RefSeq matches (N=199/267) including all the genes with defined phenotypes in Ensembl genes GRCh38 assembly (N=10). However, many protein-coding genes remain missing from the current known RefSeq gene models (N=68)Conclusion: We found many clinically relevant genes in this group of neglected genes and we anticipate that many more will be found relevant in the future. For these genes, the inaccurate label of “non-protein-coding” hinders the possibility of identifying any causal sequence variants that overlap them. In addition, Important additional annotations such as evolutionary constraint metrics are also not calculated for these genes for the same reason, further relegating them into oblivion.

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Transcription-induced formation of extrachromosomal DNA during yeast ageing

10.1101/744896 ◽

2019 ◽

Author(s):

Ryan Hull ◽

Michelle King ◽

Grazia Pizza ◽

Felix Krueger ◽

Xabier Vergara ◽

...

Keyword(s):

Copy Number ◽

De Novo ◽

Gene Copy Number ◽

Phenotypic Selection ◽

Copper Resistance ◽

Gene Copy ◽

Dna Double Strand Breaks ◽

Protein Coding ◽

Gene Copy Number Variation ◽

Number Variation

Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation, and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper resistance gene CUP1. Transcription of CUP1 causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2 / Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant we find that CUP1 eccDNA does not replicate efficiently, and high copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment.

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Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis

10.1101/751586 ◽

2019 ◽

Cited By ~ 1

Author(s):

Thomas Hackl ◽

Roman Martin ◽

Karina Barenhoff ◽

Sarah Duponchel ◽

Dominik Heider ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Gc Content ◽

Illumina Miseq ◽

Evolutionary Analysis ◽

High Quality ◽

Protein Coding ◽

Repeat Content ◽

Genome Assemblies ◽

Cafeteria Roenbergensis

AbstractThe heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99-282 × coverage per strain) and 5.09 Gb of PacBio RSII data (13-54 × coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34-36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857-8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a Bicosoecid fill an important gap in sequenced Stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists.

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