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

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined th...

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Autores principales:	Wan-Zhu Jiang, Fang-Jie Yao, Ming Fang, Li-Xin Lu, You-Min Zhang, Peng Wang, Jing-Jing Meng, Jia Lu, Xiao-Xu Ma, Qi He, Kai-Sheng Shao, Asif Ali Khan, Yun-Hui Wei
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	gloeostereum incarnatum simple sequence repeat carbohydrate-active enzymes genetic linkage map mating-type Botany QK1-989
Acceso en línea:	https://doaj.org/article/758e063ca2dd4c078b696480cfbb6e95
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spelling	oai:doaj.org-article:758e063ca2dd4c078b696480cfbb6e952021-12-01T14:40:58ZAnalysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map1229-80932092-932310.1080/12298093.2021.1954321https://doaj.org/article/758e063ca2dd4c078b696480cfbb6e952021-07-01T00:00:00Zhttp://dx.doi.org/10.1080/12298093.2021.1954321https://doaj.org/toc/1229-8093https://doaj.org/toc/2092-9323Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.Wan-Zhu JiangFang-Jie YaoMing FangLi-Xin LuYou-Min ZhangPeng WangJing-Jing MengJia LuXiao-Xu MaQi HeKai-Sheng ShaoAsif Ali KhanYun-Hui WeiTaylor & Francis Grouparticlegloeostereum incarnatumsimple sequence repeatcarbohydrate-active enzymesgenetic linkage mapmating-typeBotanyQK1-989ENMycobiology, Vol 49, Iss 4, Pp 406-420 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	gloeostereum incarnatum simple sequence repeat carbohydrate-active enzymes genetic linkage map mating-type Botany QK1-989
spellingShingle	gloeostereum incarnatum simple sequence repeat carbohydrate-active enzymes genetic linkage map mating-type Botany QK1-989 Wan-Zhu Jiang Fang-Jie Yao Ming Fang Li-Xin Lu You-Min Zhang Peng Wang Jing-Jing Meng Jia Lu Xiao-Xu Ma Qi He Kai-Sheng Shao Asif Ali Khan Yun-Hui Wei Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
description	Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.
format	article
author	Wan-Zhu Jiang Fang-Jie Yao Ming Fang Li-Xin Lu You-Min Zhang Peng Wang Jing-Jing Meng Jia Lu Xiao-Xu Ma Qi He Kai-Sheng Shao Asif Ali Khan Yun-Hui Wei
author_facet	Wan-Zhu Jiang Fang-Jie Yao Ming Fang Li-Xin Lu You-Min Zhang Peng Wang Jing-Jing Meng Jia Lu Xiao-Xu Ma Qi He Kai-Sheng Shao Asif Ali Khan Yun-Hui Wei
author_sort	Wan-Zhu Jiang
title	Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
title_short	Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
title_full	Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
title_fullStr	Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
title_full_unstemmed	Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map
title_sort	analysis of the genome sequence of strain gic-126 of gloeostereum incarnatum with genetic linkage map
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/758e063ca2dd4c078b696480cfbb6e95
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Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

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