scholarly journals Comparative genomics of Chlamydomonas

2020 ◽  
Author(s):  
Rory J. Craig ◽  
Ahmed R. Hasan ◽  
Rob W. Ness ◽  
Peter D. Keightley
Keyword(s):  
Comparative Genomics ◽  
Mating Type ◽  
Related Species ◽  
Model Organism ◽  
Functional Class ◽  
Regulatory Sequence ◽  
Centromeric Repeat ◽  
Volvocine Algae ◽  
Plant Sciences ◽  
Genome Assemblies

AbstractDespite its fundamental role as a model organism in plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources for any closely related species, obstructing its development as a study system in several fields. We present highly contiguous and well-annotated genome assemblies for the two closest known relatives of the species, Chlamydomonas incerta and Chlamydomonas schloesseri, and a third more distantly related species, Edaphochlamys debaryana. We find the three Chlamydomonas genomes to be highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as an L1 LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating-type loci of the Chlamydomonas species, potentially representing the early stages of mating-type haplotype reformation. We produce an 8-species whole-genome alignment of unicellular and multicellular volvocine algae and identify evolutionarily conserved elements in the C. reinhardtii genome. We find that short introns (<~100 bp) are extensively overlapped by conserved elements, and likely represent an important functional class of regulatory sequence in C. reinhardtii. In summary, these novel resources enable comparative genomics analyses to be performed for C. reinhardtii, significantly developing the analytical toolkit for this important model system.

scholarly journals Comparative genomics of Chlamydomonas

2021 ◽  
Author(s):  
Rory J Craig ◽  
Ahmed R Hasan ◽  
Rob W Ness ◽  
Peter D Keightley
Keyword(s):  
Comparative Genomics ◽  
Model System ◽  
Closely Related Species ◽  
Centromeric Repeat ◽  
Coccomyxa Subellipsoidea ◽  
Evolutionarily Conserved ◽  
Plant Sciences ◽  
Whole Genome Alignment ◽  
Genome Assemblies ◽  
Similar Gene

Abstract Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and &gt;260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.

scholarly journals Inferring synteny between genome assemblies: a systematic evaluation

2017 ◽  
Author(s):  
Dang Liu ◽  
Martin Hunt ◽  
Isheng. J. Tsai
Keyword(s):  
Comparative Genomics ◽  
Related Species ◽  
Gold Standard ◽  
Large Scale ◽  
Evolutionary Relationship ◽  
Systematic Evaluation ◽  
Synteny Analysis ◽  
Closely Related Species ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractIdentification of synteny between genomes of closely related species is an important aspect of comparative genomics. However, it is unknown to what extent draft assemblies lead to errors in such analysis. To investigate this, we fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests throws into question the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, determining the true evolutionary relationship is compromised by assembly improvement using a reference guided approach with a closely related species. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Our results highlight the need for gold standard genome assemblies for synteny identification and accurate downstream analysis.Author summaryGenome assemblies across all domains of life are currently produced routinely. Initial analysis of any new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. Here, we systematically evaluate this interplay by inferring synteny in genome assemblies with different degrees of contiguation. As expected, our investigation reveals that assembly quality can drastically affect synteny analysis, from the initial synteny identification to downstream analysis. Importantly, we found that improving a fragmented assembly using synteny with the genome of a related species can be dangerous, as this a priori assumes a potentially false evolutionary relationship between the species. The results presented here re-emphasize the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.

scholarly journals Meeting Highlights: Genome Sequencing and Biology 2001

2001 ◽  
Vol 2 (4) ◽  
pp. 243-251
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Genomics ◽  
Functional Genomics ◽  
Genome Sequencing ◽  
Large Scale ◽  
Model Organism

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

scholarly journals Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

2019 ◽  
Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  
Keyword(s):  
Dark Matter ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Model Organism ◽  
Technology Choice ◽  
High Quality ◽  
Sequencing Technologies ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

scholarly journals Release of a Potent Polymorphonuclear Leukocyte Chemoattractant Is Regulated by White-Opaque Switching in Candida albicans

2004 ◽  
Vol 72 (2) ◽  
pp. 667-677 ◽  
Author(s):  
Jeremy Geiger ◽  
Deborah Wessels ◽  
Shawn R. Lockhart ◽  
David R. Soll
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Candida Albicans ◽  
Mating Type ◽  
Related Species ◽  
Polymorphonuclear Leukocytes ◽  
White Phase ◽  
Bona Fide ◽  
Human Polymorphonuclear Leukocytes ◽  
Cell Chemotaxis

ABSTRACT Previous studies employing transmembrane assays suggested that Candida albicans and related species, as well as Saccharomyces cerevisiae, release chemoattractants for human polymorphonuclear leukocytes (PMNs). Because transmembrane assays do not definitively distinguish between chemokinesis and chemotaxis, single-cell chemotaxis assays were used to confirm these findings and test whether mating-type or white-opaque switching affects the release of attractant. Our results demonstrate that C. albicans, C. dubliniensis, C. tropicalis, C. parapsilosis, and C. glabrata release bona fide chemoattractants for PMNs. S. cerevisiae, however, releases a chemokinetic factor but not a chemoattractant. Characterization of the C. albicans chemoattractant revealed that it is a peptide of approximately 1 kDa. Whereas the mating type of C. albicans did not affect the release of chemoattractant, switching did. White-phase cells released chemoattractant, but opaque-phase cells did not. Since the opaque phase of C. albicans represents the mating-competent phenotype, it may be that opaque-phase cells selectively suppress the release of chemoattractant to facilitate mating.

scholarly journals Comparative Genomics Suggests Primary Homothallism of Pneumocystis Species

mBio ◽  
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
João M. G. C. F. Almeida ◽  
Ousmane H. Cissé ◽  
Álvaro Fonseca ◽  
Marco Pagni ◽  
Philippe M. Hauser
Keyword(s):  
Comparative Genomics ◽  
Sexual Reproduction ◽  
Mating Type ◽  
Fungal Pathogens ◽  
Pneumocystis Carinii ◽  
Severe Pneumonia ◽  
Genomic Region ◽  
Pneumocystis Jirovecii ◽  
Content Type

ABSTRACT   Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans. IMPORTANCE   Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.

scholarly journals MOSGA 2: Comparative genomics and validation tools

2021 ◽  
Author(s):  
Roman Martin ◽  
Hagen Dreßler ◽  
Georges Hattab ◽  
Thomas Hackl ◽  
Matthias G Fischer ◽  
...  
Keyword(s):  
Quality Control ◽  
Comparative Genomics ◽  
Data Quality ◽  
Genomic Data ◽  
Data Sets ◽  
Genomic Information ◽  
High Quality ◽  
Genome Annotations ◽  
Genome Assemblies ◽  
Annotation Quality

Due to the highly growing number of available genomic information, the need for accessible and easy-to-use analysis tools is increasing. To facilitate eukaryotic genome annotations, we created MOSGA. In this work, we show how MOSGA~2 is developed by including several advanced analyses for genomic data. Since the genomic data quality greatly impacts the annotation quality, we included multiple tools to validate and ensure high-quality user-submitted genome assemblies. Moreover, thanks to the integration of comparative genomics methods, users can benefit from a broader genomic view by analyzing multiple genomic data sets simultaneously. Further, we demonstrate the new functionalities of MOSGA~2 by different use-cases and practical examples. MOSGA~2 extends the already established application to the quality control of the genomic data and integrates and analyzes multiple genomes in a larger context, e.g., by phylogenetics.

scholarly journals Complete genomic and epigenetic maps of human centromeres

2021 ◽  
Author(s):  
Nicolas Altemose ◽  
Glennis Logsdon ◽  
Andrey V Bzikadze ◽  
Pragya Sidhwani ◽  
Sasha A Langley ◽  
...  
Keyword(s):  
Human Genome ◽  
Evolutionary Dynamics ◽  
Repetitive Sequences ◽  
Extensive Study ◽  
Sequence Evolution ◽  
Centromeric Repeat ◽  
Human Genome Assembly ◽  
Single Base Resolution ◽  
Genome Assemblies ◽  
Complete Genomic

Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, and essential role in chromosome segregation. Here, we present an extensive study of newly assembled peri/centromeric sequences representing 6.2% (189.9 Mb) of the first complete, telomere-to-telomere human genome assembly (T2T-CHM13). We discovered novel patterns of peri/centromeric repeat organization, variation, and evolution at both large and small length scales. We also found that inner kinetochore proteins tend to overlap the most recently duplicated subregions within centromeres. Finally, we compared chromosome X centromeres across a diverse panel of individuals and uncovered structural, epigenetic, and sequence variation at single-base resolution across these regions. In total, this work provides an unprecedented atlas of human centromeres to guide future studies of their complex and critical functions as well as their unique evolutionary dynamics.

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