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Lu J, Lu L, Yao F, Fang M, Ma X, Meng J, Shao K. Dicarboxylic Amino Acid Permease 7219 Regulates Fruiting Body Type of Auricularia heimuer. J Fungi (Basel) 2023; 9:876. [PMID: 37754984 PMCID: PMC10532715 DOI: 10.3390/jof9090876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Auricularia heimuer is a widely cultivated jelly mushroom. The fruiting bodies are categorized into cluster and chrysanthemum types. With changing consumer demands and the need to reduce bio-waste, the demand for clustered fruiting bodies is increasing. Therefore, gene mining for fruiting body types is a matter of urgency. We determined that the A. heimuer locus for fruiting body type was located at one end of the genetic linkage map. The locus was localized between the markers D23860 and D389 by increasing the density of the genetic linkage map. BlastN alignment showed that the marker SCL-18 was also located between D23860 and D389, and a total of 25 coding genes were annotated within this interval. Through parental transcriptome analysis and qRT-PCR verification, the locus g7219 was identified as the gene controlling the fruiting body type. A single-nucleotide substitution in the TATA box of g7219 was detected between the parents. By PCR amplification of the promoter region of g7219, the TATA-box sequences of the cluster- and chrysanthemum-type strains were found to be CATAAAA and TATAAAA, respectively. This study provides a foundation for the breeding of fruiting body types and strain improvement of A. heimuer.
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Affiliation(s)
- Jia Lu
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
- Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Lixin Lu
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Fangjie Yao
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Xiaoxu Ma
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
| | - Jingjing Meng
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Kaisheng Shao
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
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Identification of quantitative trait loci for growth traits in red swamp crayfish (Procambarus clarkii). AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Li Z, Yun L, Gao Z, Wang T, Ren X, Zhao Y. EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski. FRONTIERS IN PLANT SCIENCE 2022; 13:837787. [PMID: 35295628 PMCID: PMC8919075 DOI: 10.3389/fpls.2022.837787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/07/2022] [Indexed: 05/14/2023]
Abstract
Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei's gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot, China
| | - Zhiqi Gao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Wittmeyer KT, Oppenheim SJ, Hopper KR. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage. G3 (BETHESDA, MD.) 2021; 12:6423991. [PMID: 34751385 PMCID: PMC8727961 DOI: 10.1093/g3journal/jkab386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis made with Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies of A. atriplicis differed in contiguity, and the meta-assembly of these assemblies was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly to the point where it was also at the chromosomal-level. However, completeness of the A. atriplicis assembly, as measured by percent complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportions with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by percent complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggest greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.
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Affiliation(s)
- Kameron T Wittmeyer
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA
| | | | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA,Corresponding author: USDA-ARS, Beneficial Insect Introductions Research Unit, 501 South Chapel Street, Newark, DE 19713, USA.
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Jiang WZ, Yao FJ, Fang M, Lu LX, Zhang YM, Wang P, Meng JJ, Lu J, Ma XX, He Q, Shao KS, Khan AA, Wei YH. Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map. MYCOBIOLOGY 2021; 49:406-420. [PMID: 34512084 PMCID: PMC8409960 DOI: 10.1080/12298093.2021.1954321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Wan-Zhu Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Fang-Jie Yao
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Li-Xin Lu
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - You-Min Zhang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Jing-Jing Meng
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Jia Lu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiao-Xu Ma
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Qi He
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Kai-Sheng Shao
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Asif Ali Khan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yun-Hui Wei
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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