scholarly journals An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

Genetics ◽  
2021 ◽  
Author(s):  
Matthew E Mead ◽  
Jacob L Steenwyk ◽  
Lilian P Silva ◽  
Patrícia A de Castro ◽  
Nauman Saeed ◽  
...  
Keyword(s):  
Human Disease ◽  
Evolutionary Rate ◽  
Fungal Disease ◽  
Comparative Genomic ◽  
Genetic Elements ◽  
Genomic Approach ◽  
Evolutionary Genomic ◽  
Repeated Evolution ◽  
Species Specific ◽  
Encoding Genes

Abstract Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.

scholarly journals An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

2021 ◽  
Author(s):  
Matthew E. Mead ◽  
Jacob L. Steenwyk ◽  
Lilian P. Silva ◽  
Patrícia A. de Castro ◽  
Nauman Saeed ◽  
...  
Keyword(s):  
Human Disease ◽  
Single Copy ◽  
Fungal Disease ◽  
Comparative Genomic ◽  
Genetic Elements ◽  
Genomic Approach ◽  
Evolutionary Genomic ◽  
Repeated Evolution ◽  
Species Specific ◽  
Encoding Genes

AbstractAspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified hundreds of genes in pathogens that were faster-evolving than their orthologs in non-pathogens. For example, over 25% of all single-copy genes examined in A. fumigatus were faster-evolving. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.

scholarly journals Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants

2022 ◽  
Author(s):  
Takanori Yamashiro ◽  
Akira Shiraishi ◽  
Koji Nakayama ◽  
Honoo Satake
Keyword(s):  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Comparison ◽  
Tanacetum Cinerariifolium ◽  
The Difference ◽  
Species Specific ◽  
Distinct Features ◽  
Flanking Regions ◽  
Encoding Genes

Abstract The plant Tanacetum coccineum (painted daisy) is closely related to Tanacetum cinerariifolium (pyrethrum daisy). However, T. cinerariifolium produces large amounts of pyrethrins, a class of natural insecticides, whereas T. coccineum produces much smaller amounts of these compounds. Thus, comparative genomic analysis is expected to contribute a great deal to investigating the difference in biological defense systems, including pyrethrin biosynthesis. Here, we elucidated the 9.4-Gb draft genome of T. coccineum, consisting of 2,836,647 scaffolds and 103,680 genes. Comparative analyses of the draft genome of T. coccineum and that of T. cinerariifolium, generated in our previous study, revealed distinct features of T. coccineum genes. While the T. coccineum genome contains more numerous ribosome-inactivating protein (RIP)-encoding genes, the number of higher-toxicity type-II RIP-encoding genes is larger in T. cinerariifolium. Furthermore, the number of histidine kinases encoded by the T. coccineum genome is smaller than that of T. cinerariifolium, suggesting a biological correlation with pyrethrin biosynthesis. Moreover, the flanking regions of pyrethrin biosynthesis-related genes are also distinct between these two plants. These results provide clues to elucidation of species-specific biodefense systems, including the regulatory mechanisms underlying pyrethrin production.

scholarly journals Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 358 ◽  
Author(s):  
Fumito Maruyama ◽  
Mitsuhiko Kobata ◽  
Ken Kurokawa ◽  
Keishin Nishida ◽  
Atsuo Sakurai ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Comparative Genomic ◽  
Specific Content ◽  
Genomic Analyses ◽  
Species Specific

scholarly journals Repeated evolution of asymmetric genitalia and right-sided mating behavior in theDrosophila nannopteraspecies group

2019 ◽  
Author(s):  
Andrea Acurio ◽  
Flor T. Rhebergen ◽  
Sarah Paulus ◽  
Virginie Courtier-Orgogozo ◽  
Michael Lang
Keyword(s):  
Related Species ◽  
Current Data ◽  
The Other ◽  
Genital Morphology ◽  
Closely Related Species ◽  
Outgroup Species ◽  
Repeated Evolution ◽  
Drosophila Pachea ◽  
Species Specific ◽  
Group Species

AbstractBackgroundMale genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. TheDrosophila nannopteragroup contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species,Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown.ResultsTo assess whether the evolution of genital asymmetry could be linked to the evolution of one-sided mating, we examined phallus morphology and copulation position inD. pacheaand closely related species. The phallus was found to be symmetric in all investigated species exceptD. pachea, which display an asymmetric phallus with a right-sided gonopore, andD. acanthoptera, which harbor an asymmetrically bent phallus. In all examined species, males were found to position themselves symmetrically on top of the female, except inD. pacheaandD. nannoptera, where males mated right-sided, in distinctive, species-specific positions. In addition, the copulation duration was found to be increased innannopteragroup species compared to closely related outgroup species.ConclusionOur study shows that gains, and possibly losses, of asymmetry in genital morphology and mating position have evolved repeatedly in thenannopteragroup. Current data does not allow us to conclude whether genital asymmetry has evolved in response to changes in mating position, or vice versa.

Substitution bias and evolutionary rate of mitochondrial protein-encoding genes in four species of Cecidomyiidae

2013 ◽  
Vol 49 (12) ◽  
pp. 1183-1189
Author(s):  
Y. Duan ◽  
R. H. Wu ◽  
Y. L. Jiang ◽  
T. Li ◽  
Y. Q. Wu ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Mitochondrial Protein ◽  
Protein Encoding ◽  
Substitution Bias ◽  
Encoding Genes

scholarly journals The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisong Hu ◽  
Zhongping Xu ◽  
Maojun Wang ◽  
Rui Fan ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Families ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Phylogenomic Analysis ◽  
Genomic Analyses ◽  
Species Specific ◽  
Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

scholarly journals Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 307 ◽  
Author(s):  
María Santamaría ◽  
Pedro Hernández-Crespo ◽  
Félix Ortego ◽  
Vojislava Grbic ◽  
Miodrag Grbic ◽  
...  
Keyword(s):  
Tetranychus Urticae ◽  
Comparative Genomic ◽  
Comparative Genomic Approach ◽  
Genomic Approach ◽  
Cysteine Peptidases

scholarly journals The Fission Yeast Rad32 (Mre11)-Rad50-Nbs1 Complex Is Required for the S-Phase DNA Damage Checkpoint

2003 ◽  
Vol 23 (18) ◽  
pp. 6564-6573 ◽  
Author(s):  
Charly Chahwan ◽  
Toru M. Nakamura ◽  
Sasirekha Sivakumar ◽  
Paul Russell ◽  
Nicholas Rhind
Keyword(s):  
Dna Damage ◽  
Fission Yeast ◽  
Chromosome Instability ◽  
S Phase ◽  
Comparative Genomic ◽  
Dna Damage Checkpoint ◽  
Checkpoint Signaling ◽  
Damage Repair ◽  
Genomic Approach ◽  
Telomere Regulation

ABSTRACT Mre11, Rad50, and Nbs1 form a conserved heterotrimeric complex that is involved in recombination and DNA damage checkpoints. Mutations in this complex disrupt the S-phase DNA damage checkpoint, the checkpoint which slows replication in response to DNA damage, and cause chromosome instability and cancer in humans. However, how these proteins function and specifically where they act in the checkpoint signaling pathway remain crucial questions. We identified fission yeast Nbs1 by using a comparative genomic approach and showed that the genes for human Nbs1 and fission yeast Nbs1 and that for their budding yeast counterpart, Xrs2, are members of an evolutionarily related but rapidly diverging gene family. Fission yeast Nbs1, Rad32 (the homolog of Mre11), and Rad50 are involved in DNA damage repair, telomere regulation, and the S-phase DNA damage checkpoint. However, they are not required for G2 DNA damage checkpoint. Our results suggest that a complex of Rad32, Rad50, and Nbs1 acts specifically in the S-phase branch of the DNA damage checkpoint and is not involved in general DNA damage recognition or signaling.

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