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On February 15, 2021, JGG published online a research paper entitled "Identifying a melanogenesis-related candidate gene by a high quality genome assembly and population diversity analysis in Hypsizygus marmoreus" by Zhang Jisen's research team from the Genome and Biotechnology Research Center of Fujian Agriculture and Forestry University .
This study analyzed the chromosome-level genome of Shimeji mushroom for the first time, clarified the evolutionary position of Shimeji mushroom in the phylum Basidiomycota, and identified related genes that control the gray-white color of the strain.
DOI: https://doi.
org/10.
1016/j.
jgg.
2021.
01.
002 Shimeji mushroom is one of the important edible fungi for factory planting.
There are two strains of gray and white.
The white albino cultivars with gray strains have weaker growth speed and resistance than gray cultivars, but the relationship between their genome evolution and the genetic mechanism of differentiation between white and gray strains is still unclear.
The study first completed the chromosome-level genome assembly of Shimeji mushroom, which is 43.
7 Mb in size and contains 12 chromosomes.
Contig N50 reaches 2.
14 Mb and contains 14,944 protein-coding genes.
BUSCO assesses its completeness as 97.
6%.
Phylogenetic tree and molecular clock analysis showed that Agaricus originated about 140.
7 million years ago.
The relationship between Shimeji mushroom and Coprinus comatus was the closest, and the two differentiated 70.
6 million years ago.
Comparative genomics analysis showed that the chromosome structure of Agaricidae was relatively conserved.
The genome of Agaricaceae and Basidiomycetes had undergone multiple chromosome breaks, fusions and replication events after the division of Agaricus and Basidiomycetes.Through re-sequencing of the Pseudomonas group, multiple evidences show that there are four main subgroups of P.
The combined analysis based on genetic variation and morphological characteristics further indicates that the white strain is an albino variety of the gray strain, rather than an independent origin.
(A) Shimeji mushroom chromosome circle; (B) Shimeji mushroom population principal component analysis; (C) Shishiji mushroom population structure diagram; (D) Gray and white strain cross and selfed population construction model; (E) Candidate interval Localization, genotype analysis and expression analysis of genes related to melanin.
In order to explore the formation mechanism of the white strains of Shimeji mushroom, the author constructed a hybrid and selfed genetic population of parents Hm88 (white) and Hm61 (grey).
In F2 progeny, the separation ratio of white and gray traits is about 1:3, indicating that color is a quality trait controlled by a single gene.
Through QTL mapping (BSA), population genotype analysis, transcriptome sequencing and other multi-omics joint analysis, the 0.
6 Mb candidate region of chromosome 6 has 6 non-synonymous mutations in the candidate region, which is consistent with the gray and white strains.
The genetic law of genotype in natural population and progeny.
One of the cytochrome P450 candidate genes (HM01_091350) is involved in the synthesis of melanin in the L-dopa pathway in gray strains, and is a key gene that controls the formation of melanin.
The study collected 92 different strains from China, which enriched the germplasm resource bank of Shimeji mushroom.
Assemble high-quality genomes to analyze the evolutionary relationship of Shimeji mushroom from the perspective of population genetics.
Linking genetic variation with morphological characteristics provides valuable resources for genetic research and variety improvement of Shimeji mushroom.
The identification of genes related to melanin metabolism provides a theoretical basis for the study of the color formation mechanism of edible fungi.
Dr.
Gang Wang from the Genome and Biotechnology Research Center of Fujian Agriculture and Forestry University is the first author, and Professor Zhang Jisen is the corresponding author.
Dr.
Chen Lianfu from South China Botanical Garden, Chinese Academy of Sciences, Dr.
Tang Weiqi from Minjiang University, Wang Yuanyuan, a graduate student of Fujian Agriculture and Forestry University, Professor Xie Guigui and Professor Liu Zhongjian from Fujian Agriculture and Forestry University, and Professor Ming Ruiguang from the University of Illinois, USA participated in this research. This research has won the major agricultural technology extension service pilot project of the edible fungus industry in Fujian Province (KNJ-153011-1), and the genetic engineering improvement project of important economic crops (pineapple, real mushroom, tea) in Fujian (726430923-2016NZ0001-1/04) support.
This article is reproduced from the Public Account of JGG Genetics, Plant Biotechnology Pbj Exchange Group.
In order to more effectively help the majority of scientific researchers to obtain relevant information, Plant Biotechnology Pbj has established a WeChat group, Plant Biotechnology Journal submissions and document-related issues, and the public account is released.
The content and public account submission questions will be concentrated in the group for answers, and at the same time, academic exchanges and collision thinking in the group are encouraged.
In order to ensure a good discussion environment in the group, please add the editor WeChat first, scan the QR code to add, and then we will promptly invite you to join the group.
Tips: When adding the editor WeChat and after joining the group, please be sure to note the school or unit + name, and the PI should be noted at the end, and we will invite you to join the PI group.
This study analyzed the chromosome-level genome of Shimeji mushroom for the first time, clarified the evolutionary position of Shimeji mushroom in the phylum Basidiomycota, and identified related genes that control the gray-white color of the strain.
DOI: https://doi.
org/10.
1016/j.
jgg.
2021.
01.
002 Shimeji mushroom is one of the important edible fungi for factory planting.
There are two strains of gray and white.
The white albino cultivars with gray strains have weaker growth speed and resistance than gray cultivars, but the relationship between their genome evolution and the genetic mechanism of differentiation between white and gray strains is still unclear.
The study first completed the chromosome-level genome assembly of Shimeji mushroom, which is 43.
7 Mb in size and contains 12 chromosomes.
Contig N50 reaches 2.
14 Mb and contains 14,944 protein-coding genes.
BUSCO assesses its completeness as 97.
6%.
Phylogenetic tree and molecular clock analysis showed that Agaricus originated about 140.
7 million years ago.
The relationship between Shimeji mushroom and Coprinus comatus was the closest, and the two differentiated 70.
6 million years ago.
Comparative genomics analysis showed that the chromosome structure of Agaricidae was relatively conserved.
The genome of Agaricaceae and Basidiomycetes had undergone multiple chromosome breaks, fusions and replication events after the division of Agaricus and Basidiomycetes.Through re-sequencing of the Pseudomonas group, multiple evidences show that there are four main subgroups of P.
The combined analysis based on genetic variation and morphological characteristics further indicates that the white strain is an albino variety of the gray strain, rather than an independent origin.
(A) Shimeji mushroom chromosome circle; (B) Shimeji mushroom population principal component analysis; (C) Shishiji mushroom population structure diagram; (D) Gray and white strain cross and selfed population construction model; (E) Candidate interval Localization, genotype analysis and expression analysis of genes related to melanin.
In order to explore the formation mechanism of the white strains of Shimeji mushroom, the author constructed a hybrid and selfed genetic population of parents Hm88 (white) and Hm61 (grey).
In F2 progeny, the separation ratio of white and gray traits is about 1:3, indicating that color is a quality trait controlled by a single gene.
Through QTL mapping (BSA), population genotype analysis, transcriptome sequencing and other multi-omics joint analysis, the 0.
6 Mb candidate region of chromosome 6 has 6 non-synonymous mutations in the candidate region, which is consistent with the gray and white strains.
The genetic law of genotype in natural population and progeny.
One of the cytochrome P450 candidate genes (HM01_091350) is involved in the synthesis of melanin in the L-dopa pathway in gray strains, and is a key gene that controls the formation of melanin.
The study collected 92 different strains from China, which enriched the germplasm resource bank of Shimeji mushroom.
Assemble high-quality genomes to analyze the evolutionary relationship of Shimeji mushroom from the perspective of population genetics.
Linking genetic variation with morphological characteristics provides valuable resources for genetic research and variety improvement of Shimeji mushroom.
The identification of genes related to melanin metabolism provides a theoretical basis for the study of the color formation mechanism of edible fungi.
Dr.
Gang Wang from the Genome and Biotechnology Research Center of Fujian Agriculture and Forestry University is the first author, and Professor Zhang Jisen is the corresponding author.
Dr.
Chen Lianfu from South China Botanical Garden, Chinese Academy of Sciences, Dr.
Tang Weiqi from Minjiang University, Wang Yuanyuan, a graduate student of Fujian Agriculture and Forestry University, Professor Xie Guigui and Professor Liu Zhongjian from Fujian Agriculture and Forestry University, and Professor Ming Ruiguang from the University of Illinois, USA participated in this research. This research has won the major agricultural technology extension service pilot project of the edible fungus industry in Fujian Province (KNJ-153011-1), and the genetic engineering improvement project of important economic crops (pineapple, real mushroom, tea) in Fujian (726430923-2016NZ0001-1/04) support.
This article is reproduced from the Public Account of JGG Genetics, Plant Biotechnology Pbj Exchange Group.
In order to more effectively help the majority of scientific researchers to obtain relevant information, Plant Biotechnology Pbj has established a WeChat group, Plant Biotechnology Journal submissions and document-related issues, and the public account is released.
The content and public account submission questions will be concentrated in the group for answers, and at the same time, academic exchanges and collision thinking in the group are encouraged.
In order to ensure a good discussion environment in the group, please add the editor WeChat first, scan the QR code to add, and then we will promptly invite you to join the group.
Tips: When adding the editor WeChat and after joining the group, please be sure to note the school or unit + name, and the PI should be noted at the end, and we will invite you to join the PI group.
