Macrosynteny Analysis Between Lentinula Edodes and Lentinula Novae-zelandiae Reveals Signals of Domestication in Lentinula Edodes

Overview

Journal Sci Rep

Specialty Science

Date 2021 May 11

PMID 33972587

Citations 4

Authors

Christopher Alan Smith

Affiliations

Soon will be listed here.

Abstract

The basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

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References

Fierst J, Murdock D . Decontaminating eukaryotic genome assemblies with machine learning. BMC Bioinformatics. 2017; 18(1):533. PMC: 5709863. DOI: 10.1186/s12859-017-1941-0. View

Drillon G, Carbone A, Fischer G . SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS One. 2014; 9(3):e92621. PMC: 3961402. DOI: 10.1371/journal.pone.0092621. View

Li C, Gong W, Zhang L, Yang Z, Nong W, Bian Y . Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in , Shiitake Mushroom. Front Microbiol. 2017; 8:237. PMC: 5314409. DOI: 10.3389/fmicb.2017.00237. View

Wu L, van Peer A, Song W, Wang H, Chen M, Tan Q . Cloning of the Lentinula edodes B mating-type locus and identification of the genetic structure controlling B mating. Gene. 2013; 531(2):270-8. DOI: 10.1016/j.gene.2013.08.090. View

Liang Y, Lu D, Wang S, Zhao Y, Gao S, Han R . Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea. Genomics Proteomics Bioinformatics. 2020; 18(3):341-351. PMC: 7801210. DOI: 10.1016/j.gpb.2018.10.009. View

James T, Sun S, Li W, Heitman J, Kuo H, Lee Y . Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Mycologia. 2013; 105(6):1374-90. DOI: 10.3852/13-162. View

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D . Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. PMC: 2752132. DOI: 10.1101/gr.092759.109. View

Kwan H, Xu H . Construction of a genetic linkage map of shiitake mushroom Lentinula edodes strain L-54. J Biochem Mol Biol. 2002; 35(5):465-71. DOI: 10.5483/bmbrep.2002.35.5.465. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

10.

Chan P, Lowe T . tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019; 1962:1-14. PMC: 6768409. DOI: 10.1007/978-1-4939-9173-0_1. View

11.

Gong W, Liu W, Lu Y, Bian Y, Zhou Y, Kwan H . Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes. Fungal Biol. 2014; 118(3):295-308. DOI: 10.1016/j.funbio.2014.01.001. View

12.

Gong W, Li L, Zhou Y, Bian Y, Kwan H, Cheung M . Detection of Quantitative Trait Loci Underlying Yield-Related Traits in Shiitake Culinary-Medicinal Mushroom, Lentinus edodes (Agaricomycetes). Int J Med Mushrooms. 2018; 20(5):451-458. DOI: 10.1615/IntJMedMushrooms.2018026236. View

13.

Grabherr M, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F . Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics. 2010; 26(9):1145-51. PMC: 2859124. DOI: 10.1093/bioinformatics/btq102. View

14.

Vurture G, Sedlazeck F, Nattestad M, Underwood C, Fang H, Gurtowski J . GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017; 33(14):2202-2204. PMC: 5870704. DOI: 10.1093/bioinformatics/btx153. View

15.

Kim J, Kim D, Park Y, Jang M . Transcriptome analysis of the edible mushroom Lentinula edodes in response to blue light. PLoS One. 2020; 15(3):e0230680. PMC: 7100940. DOI: 10.1371/journal.pone.0230680. View

16.

Shim D, Park S, Kim K, Bae W, Lee G, Ha B . Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol. 2016; 223:24-5. DOI: 10.1016/j.jbiotec.2016.02.032. View

17.

Ha B, Kim S, Kim M, Moon Y, Song Y, Ryu J . Diversity of A mating type in Lentinula edodes and mating type preference in the cultivated strains. J Microbiol. 2018; 56(6):416-425. DOI: 10.1007/s12275-018-8030-6. View

18.

Castanera R, Lopez-Varas L, Borgognone A, Labutti K, Lapidus A, Schmutz J . Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet. 2016; 12(6):e1006108. PMC: 4905642. DOI: 10.1371/journal.pgen.1006108. View

19.

Luo J, Lyu M, Chen R, Zhang X, Luo H, Yan C . SLR: a scaffolding algorithm based on long reads and contig classification. BMC Bioinformatics. 2019; 20(1):539. PMC: 6820941. DOI: 10.1186/s12859-019-3114-9. View

20.

Steenwyk J, Rokas A . Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation. Front Microbiol. 2018; 9:288. PMC: 5826948. DOI: 10.3389/fmicb.2018.00288. View