scholarly journals Chromosomal Translocation and Segmental Duplication in Cryptococcus neoformans

2005 ◽  
Vol 4 (2) ◽  
pp. 401-406 ◽  
Author(s):  
James A. Fraser ◽  
Johnny C. Huang ◽  
Read Pukkila-Worley ◽  
J. Andrew Alspaugh ◽  
Thomas G. Mitchell ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Segmental Duplication ◽  
Chromosomal Translocation ◽  
Genome Project ◽  
Fungal Genome ◽  
Segmental Duplications ◽  
Physical Evidence ◽  
A Genome ◽  
Strain Pair ◽  
Meiotic Mapping

ABSTRACT Large chromosomal events such as translocations and segmental duplications enable rapid adaptation to new environments. Here we marshal genomic, genetic, meiotic mapping, and physical evidence to demonstrate that a chromosomal translocation and segmental duplication occurred during construction of a congenic strain pair in the fungal human pathogen Cryptococcus neoformans. Two chromosomes underwent telomere-telomere fusion, generating a dicentric chromosome that broke to produce a chromosomal translocation, forming two novel chromosomes sharing a large segmental duplication. The duplication spans 62,872 identical nucleotides and generated a second copy of 22 predicted genes, and we hypothesize that this event may have occurred during meiosis. Gene disruption studies of one embedded gene (SMG1) corroborate that this region is duplicated in an otherwise haploid genome. These findings resolve a genome project assembly anomaly and illustrate an example of rapid genome evolution in a fungal genome rich in repetitive elements.

RNA Interference in the Pathogenic Fungus Cryptococcus neoformans

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 463-470
Author(s):  
Hong Liu ◽  
Tricia R Cottrell ◽  
Lynda M Pierini ◽  
William E Goldman ◽  
Tamara L Doering
Keyword(s):  
Rna Interference ◽  
Cryptococcus Neoformans ◽  
Pathogenic Fungus ◽  
Experimental System ◽  
Technical Difficulty ◽  
Genome Project ◽  
Specific Gene ◽  
Mrna Levels ◽  
Double Stranded Rna ◽  
A Genome

Abstract Cryptococcus neoformans is a pathogenic fungus responsible for serious disease in immunocompromised individuals. This organism has recently been developed as an experimental system, with initiation of a genome project among other molecular advances. However, investigations of Cryptococcus are hampered by the technical difficulty of specific gene replacements. RNA interference, a process in which the presence of double-stranded RNA homologous to a gene of interest results in specific degradation of the corresponding message, may help solve this problem. We have shown that expression of double-stranded RNA corresponding to portions of the cryptococcal CAP59 and ADE2 genes results in reduced mRNA levels for those genes, with phenotypic consequences similar to that of gene disruption. The two genes could also be subjected to simultaneous interference through expression of chimeric double-stranded RNA. Specific modulation of protein expression through introduction of double-stranded RNA thus operates in C. neoformans, which is the first demonstration of this technique in a fungal organism. Use of RNA interference in Cryptococcus should allow manipulation of mRNA levels for functional analysis of genes of interest and enable efficient exploration of genes discovered by genome sequencing.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

scholarly journals Dblox: a genome-wide test for ancient segmental duplication

2004 ◽  
Vol 20 (16) ◽  
pp. 2834-2835 ◽  
Author(s):  
R. Friedman ◽  
V. Ekollu ◽  
J. R. Rose ◽  
A. L. Hughes
Keyword(s):  
Segmental Duplication ◽  
Genome Wide ◽  
A Genome

scholarly journals Korean Genome Project: 1094 Korean personal genomes with clinical information

2020 ◽  
Vol 6 (22) ◽  
pp. eaaz7835 ◽  
Author(s):  
Sungwon Jeon ◽  
Youngjune Bhak ◽  
Yeonsong Choi ◽  
Yeonsu Jeon ◽  
Seunghoon Kim ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Imputation Accuracy ◽  
Clinical Information ◽  
Genome Project ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Whole Genomes ◽  
Personal Genomes

We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

A water channel of the nematode C. elegans and its implications for channel selectivity of MIP proteins

1998 ◽  
Vol 275 (6) ◽  
pp. C1459-C1464 ◽  
Author(s):  
Michio Kuwahara ◽  
Kenichi Ishibashi ◽  
Yong Gu ◽  
Yoshio Terada ◽  
Yuji Kohara ◽  
...  
Keyword(s):  
Amino Acid ◽  
Water Channel ◽  
Genome Project ◽  
Amino Acid Residues ◽  
C Elegans ◽  
Extra Amino Acid ◽  
Urea Permeability ◽  
Glycerol Facilitator ◽  
A Genome ◽  
Channel Selectivity

A genome project focusing on the nematode Caenorhabditis elegans has demonstrated the presence of eight cDNAs belonging to the major intrinsic protein superfamily. We functionally characterized one of these cDNAs named C01G6.1. Injection of C01G6.1 cRNA increased the osmotic water permeability ( P f) of Xenopusoocytes 11-fold and the urea permeability 4.5-fold but failed to increase the glycerol permeability. It has been speculated that the MIP family may be separated into two large subfamilies based on the presence or absence of two segments of extra amino acid residues (∼15 amino acids) at the second and third extracellular loops. Because C01G6.1 (designated AQP-CE1), AQP3, and glycerol facilitator (GlpF) all have these two segments, we replaced the segments of AQP-CE1 with those of AQP3 and GlpF to identify their roles. The functional characteristics of these mutants were principally similar to that of wild-type AQP-CE1, although the values of P f and urea permeability were decreased by 39–74% and 28–65%, respectively. These results suggest that the two segments of extra amino acid residues may not contribute to channel selectivity or formation of the route for small solutes.

scholarly journals Cryptococcus neoformans Typing by PCR Fingerprinting Using (GACA)4 Primers Based on C. neoformans Genome Project Data

2007 ◽  
Vol 45 (10) ◽  
pp. 3427-3430 ◽  
Author(s):  
M. Cogliati ◽  
M. C. Esposto ◽  
G. Liberi ◽  
A. M. Tortorano ◽  
M. A. Viviani
Keyword(s):  
Cryptococcus Neoformans ◽  
Genome Project ◽  
Pcr Fingerprinting ◽  
Project Data ◽  
Genome Project Data

scholarly journals Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10457
Author(s):  
Xianwen Meng ◽  
Ting Yang ◽  
Jing Liu ◽  
Mingde Zhao ◽  
Jiuli Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

scholarly journals Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice

2020 ◽  
Vol 16 ◽  
pp. 117693432094149
Author(s):  
Jun Yang ◽  
Peng Xu ◽  
Diqiu Yu
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Japonica Rice ◽  
Segmental Duplications ◽  
Related Sequence ◽  
Genome Wide ◽  
A Genome

Rice ( Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.

scholarly journals Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production

2020 ◽  
Vol 10 (10) ◽  
pp. 3515-3531 ◽  
Author(s):  
Jake C. Fountain ◽  
Josh P. Clevenger ◽  
Brian Nadon ◽  
Ramey C. Youngblood ◽  
Walid Korani ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Phylogenetic Analyses ◽  
Aflatoxin Production ◽  
Genome Project ◽  
Fungal Genome ◽  
Bzip Transcription Factor ◽  
Important Species ◽  
Long Read ◽  
Phylogenomic Analyses ◽  
Reference Genomes

Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae. However, less progress has been made for A. flavus. As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus. Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference-grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 60 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.

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