Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

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The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species

PLoS ONE ◽

10.1371/journal.pone.0255091 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255091

Author(s):

Sadaf Habib ◽

Shanshan Dong ◽

Yang Liu ◽

Wenbo Liao ◽

Shouzhou Zhang

Keyword(s):

Mitochondrial Genome ◽

Vascular Plants ◽

Southern China ◽

Complete Mitochondrial Genome ◽

Vascular Plant ◽

Mitochondrial Protein ◽

Rrna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Evolutionary Features

Mitochondrial genomes of vascular plants are well known for their liability in architecture evolution. However, the evolutionary features of mitogenomes at intra-generic level are seldom studied in vascular plants, especially among gymnosperms. Here we present the complete mitogenome of Cycas debaoensis, an endemic cycad species to the Guangxi region in southern China. In addition to assemblage of draft mitochondrial genome, we test the conservation of gene content and mitogenomic stability by comparing it to the previously published mitogenome of Cycas taitungensis. Furthermore, we explored the factors such as structural rearrangements and nuclear surveillance of double-strand break repair (DSBR) proteins in Cycas in comparison to other vascular plant groups. The C. debaoensis mitogenome is 413,715 bp in size and encodes 69 unique genes, including 40 protein coding genes, 26 tRNAs, and 3 rRNA genes, similar to that of C. taitungensis. Cycas mitogenomes maintained the ancestral intron content of seed plants (26 introns), which is reduced in other lineages of gymnosperms, such as Ginkgo biloba, Taxus cuspidata and Welwitschia mirabilis due to selective pressure or retroprocessing events. C. debaoensis mitogenome holds 1,569 repeated sequences (> 50 bp), which partially account for fairly large intron size (1200 bp in average) of Cycas mitogenome. The comparison of RNA-editing sites revealed 267 shared non-silent editing site among predicted vs. empirically observed editing events. Another 33 silent editing sites from empirical data increase the total number of editing sites in Cycas debaoensis mitochondrial protein coding genes to 300. Our study revealed unexpected conserved evolution between the two Cycas species. Furthermore, we found strict collinearity of the gene order along with the identical set of genomic content in Cycas mt genomes. The stability of Cycas mt genomes is surprising despite the existence of large number of repeats. This structural stability may be related to the relative expansion of three DSBR protein families (i.e., RecA, OSB, and RecG) in Cycas nuclear genome, which inhibit the homologous recombinations, by monitoring the accuracy of mitochondrial chromosome repair.

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Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves

Phytopathology ◽

10.1094/phyto-12-19-0452-r ◽

2020 ◽

Vol 110 (7) ◽

pp. 1260-1269

Author(s):

Fang-Fang Fu ◽

Zhaodong Hao ◽

Pengkai Wang ◽

Ye Lu ◽

Liang-Jiao Xue ◽

...

Keyword(s):

Structure Prediction ◽

Polyketide Synthase ◽

Colletotrichum Gloeosporioides ◽

Genomic Analysis ◽

Enrichment Analysis ◽

Comparative Genomic ◽

Pathway Enrichment Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Species Specific

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.

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