Genome Sequence Analysis of Auricularia heimuer Combined with Genetic Linkage Map

Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. By combining the genome sequence analysis with the genetic linkage map, the mating-type locus of A. heimuer was located on scaffold45 and consisted of two subunits, α and β. Each subunit consisted of a pair of homeodomain mating-type protein genes HD1 and HD2. The mapping revealed conserved synteny at the whole mating-type loci and mirror symmetry relations near the β subunit between A. heimuer and Exidia glandulosa. This study proposed the potential for the bioethanol production by consolidated bioprocessing of A. heimuer. It will promote understanding of the lignocellulose degradation system and facilitate more efficient conversion of the agricultural wastes used for mushroom cultivation. It also will advance the research on the fruiting body development and evolution of A. heimuer.

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A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

BMC Genomics ◽

10.1186/s12864-017-4421-z ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 9

Author(s):

Wei Gao ◽

Jibin Qu ◽

Jinxia Zhang ◽

Anton Sonnenberg ◽

Qiang Chen ◽

...

Keyword(s):

Linkage Map ◽

Mating Type ◽

Physical Mapping ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

De Novo

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Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L

PLoS ONE ◽

10.1371/journal.pone.0064799 ◽

2013 ◽

Vol 8 (5) ◽

pp. e64799 ◽

Cited By ~ 66

Author(s):

Huaan Yang ◽

Ye Tao ◽

Zequn Zheng ◽

Qisen Zhang ◽

Gaofeng Zhou ◽

...

Keyword(s):

Linkage Map ◽

Genome Sequence ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Draft Genome ◽

Lupinus Angustifolius ◽

Draft Genome Sequence ◽

Crop Species ◽

Legume Crop

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A genetic linkage map of Pleurotus pulmonarius based on AFLP markers, and localization of the gene region for the sporeless mutation

Genome ◽

10.1139/g09-021 ◽

2009 ◽

Vol 52 (5) ◽

pp. 438-446 ◽

Cited By ~ 16

Author(s):

Yasuhito Okuda ◽

Shigeyuki Murakami ◽

Teruyuki Matsumoto

Keyword(s):

Linkage Map ◽

Mating Type ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Natural Populations ◽

Aflp Markers ◽

Gene Region ◽

Pleurotus Pulmonarius ◽

Type Factor ◽

Enormous Number

In the cultivation of edible mushrooms, including Pleurotus pulmonarius (Fr.) Quel., the enormous number of spores produced by fruiting bodies can adversely affect mushroom growers’ health, mushroom cultivation facilities, and the genetic diversity of natural populations. In this study, we constructed a primary genetic linkage map and identified the locus associated with the sporulation-deficient (sporeless) mutation of P. pulmonarius using 150 progeny isolates derived from a cross between sporeless and wild-type isolates. Based on the segregation of 300 AFLP markers, two mating-type factors, and the sporeless trait, a linkage map was generated consisting of 12 linkage groups. The map covered a total genetic distance of 971 cM, with an average marker interval of 5.2 cM. The gene region responsible for the sporeless mutation was located in linkage group II including 40 AFLP markers and the A mating-type factor locus. Of these markers, the nearest marker to the sporeless locus was located 1.4 cM away. Construction of this P. pulmonarius genetic linkage map and identification of markers that are closely linked to the sporeless locus will facilitate marker-assisted selective breeding of a sporeless strain with economically important traits.

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Location on the Human Genetic Linkage Map of 26 Genes Involved in Blood Coagulation

Thrombosis and Haemostasis ◽

10.1055/s-0038-1656070 ◽

1997 ◽

Vol 77 (05) ◽

pp. 0873-0878 ◽

Cited By ~ 9

Author(s):

Bobby P C Koeleman ◽

Pieter H Reitsma ◽

Egbert Bakker ◽

Rogier M Bertina

Keyword(s):

Linkage Map ◽

Blood Coagulation ◽

Candidate Genes ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Coagulation Cascade ◽

Candidate Gene Approach ◽

Genotype Data ◽

Genetic Linkage Analysis ◽

Linkage Maps

SummarySeveral human genetic linkage maps have been constructed as part of the Human Genome Project. These maps show the positional order of closely linked, highly informative AC-repeat polymorphisms on each human chromosome, and are extremely useful in genetic linkage analysis of inheritable diseases. For a candidate gene approach the current linkage maps are less useful, since they consist mainly of anonymous markers rather than of specific genes. This situation also applies for inheritable disorders of blood coagulation. Numerous genes are involved in the blood coagulation cascade and its regulation, and can be considered as candidate genes for unexplained haemophilia and thrombophilia. We have selected 29 candidate genes that seem to be the ones most likely to be involved in thrombophilia. For 19 genes genotype data were already present in the CEPH database (version 7.0). We typed 7 additional genes in the CEPH reference families, i.e. the factor V, factor XII, protein C, protein S, prothrombin, thrombomodulin, and heparin cofactor II gene. The genotype data were used to integrate these 26 genes in the current genetic linkage map, and to identify closely linked AC-repeat polymorphisms. This information will benefit the investigation of inheritable disorders of blood coagulation, especially thrombophilia.

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A Genome Sequence Survey Shows that the Pathogenic Yeast Candida parapsilosis Has a Defective MTLa1 Allele at Its Mating Type Locus

Eukaryotic Cell ◽

10.1128/ec.4.6.1009-1017.2005 ◽

2005 ◽

Vol 4 (6) ◽

pp. 1009-1017 ◽

Cited By ~ 46

Author(s):

Mary E. Logue ◽

Simon Wong ◽

Kenneth H. Wolfe ◽

Geraldine Butler

Keyword(s):

Genome Sequence ◽

Mating Type ◽

Type Strain ◽

Candida Parapsilosis ◽

Type Locus ◽

Stop Codons ◽

Mating Type Locus ◽

Genome Sequence Survey ◽

A Genome ◽

Mating Pathway

ABSTRACT Candida parapsilosis is responsible for ca. 15% of Candida infections and is of particular concern in neonates and surgical intensive care patients. The related species Candida albicans has recently been shown to possess a functional mating pathway. To analyze the analogous pathway in C. parapsilosis, we carried out a genome sequence survey of the type strain. We identified ca. 3,900 genes, with an average amino acid identity of 59% with C. albicans. Of these, 23 are predicted to be predominantly involved in mating. We identified a genomic locus homologous to the MTL a mating type locus of C. albicans, but the C. parapsilosis type strain has at least two internal stop codons in the MTL a 1 open reading frame, and two predicted introns are not spliced. These stop codons were present in MTL a 1 of all eight C. parapsilosis isolates tested. Furthermore, we found that all isolates of C. parapsilosis tested appear to contain only the MTL a idiomorph at the presumptive mating locus, unlike C. albicans and C. dubliniensis. MTLα sequences are present but at a different chromosomal location. It is therefore likely that all (or at least the majority) of C. parapsilosis isolates have a mating pathway that is either defective or substantially different from that of C. albicans.

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Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Mycobiology ◽

10.1080/12298093.2021.1954321 ◽

2021 ◽

pp. 1-15

Author(s):

Wan-Zhu Jiang ◽

Fang-Jie Yao ◽

Ming Fang ◽

Li-Xin Lu ◽

You-Min Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genome Sequence ◽

Genetic Linkage ◽

Genetic Linkage Map

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A Combined Amplified Fragment Length Polymorphism and Randomly Amplified Polymorphism DNA Genetic Linkage Map of Mycosphaerella graminicola, the Septoria Tritici Leaf Blotch Pathogen of Wheat

Genetics ◽

10.1093/genetics/161.4.1497 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1497-1505

Author(s):

Gert H J Kema ◽

Stephen B Goodwin ◽

Sonia Hamza ◽

Els C P Verstappen ◽

Jessica R Cavaletto ◽

...

Keyword(s):

Molecular Markers ◽

Linkage Map ◽

Mating Type ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Mycosphaerella Graminicola ◽

Septoria Tritici ◽

Biological Traits ◽

Linkage Groups

Abstract An F1 mapping population of the septoria tritici blotch pathogen of wheat, Mycosphaerella graminicola, was generated by crossing the two Dutch field isolates IPO323 and IPO94269. AFLP and RAPD marker data sets were combined to produce a high-density genetic linkage map. The final map contained 223 AFLP and 57 RAPD markers, plus the biological traits mating type and avirulence, in 23 linkage groups spanning 1216 cM. Many AFLPs and some RAPD markers were clustered. When markers were reduced to 1 per cluster, 229 unique positions were mapped, with an average distance of 5.3 cM between markers. Because M. graminicola probably has 17 or 18 chromosomes, at least 5 of the 23 linkage groups probably will need to be combined with others once additional markers are added to the map. This was confirmed by pulsed-field gel analysis; probes derived from 2 of the smallest linkage groups hybridized to two of the largest chromosome-sized bands, revealing a discrepancy between physical and genetic distance. The utility of the map was demonstrated by identifying molecular markers tightly linked to two genes of biological interest, mating type and avirulence. Bulked segregant analysis was used to identify additional molecular markers closely linked to these traits. This is the first genetic linkage map for any species in the genus Mycosphaerella or the family Mycosphaerellaceae.

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