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Lactarius is one of the most prominent genera of mushroom-forming fungi in the world. In the present study, complete mitochondrial genomes (mitogenomes) from six Lactarius species were sequenced and assembled. The six mitogenomes were all composed of circular DNA molecules, with total lengths ranging from 38,445 bp to 60,843 bp. The GC contents, GC skews, and AT skews of the mitogenomes varied among the six species. Mitogenomic synteny analysis revealed the presence of gene rearrangements among the mitogenomes. Among the 15 core protein coding genes (PCGs) within the mitogenomes, nad4L exhibited the least genetic distance among species, indicating a high degree of conservation. In addition, the Ka/Ks values for all 15 core PCGs were <1, suggesting that they were subject to purifying selection. Comparative analyses indicated that the increase of intron numbers and sizes contributed to the expansion of mitogenomes in Lactarius. Phylogenetic analyses based on three combined gene datasets yielded identical and well-supported (BPP ≥ 0.83) topologies, dividing the six Lactarius species into two groups. This study provides the first report of mitogenomes from Lactarius and promotes further understanding of the genetics, evolution, and phylogenetic relationships of this important ectomycorrhizal fungal genus.
Pubmed ID: 30308282
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Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
View all literature mentionsA software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
View all literature mentionsMethod for mitochondrial baiting and iterative mapping. MITObim assembles novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.
View all literature mentionsSoftware tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
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