Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae)

Abstract

Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9–81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.

Taxonomy, Phylogeny, Divergence Time Estimation, and Biogeography of the Family Pseudoplagiostomataceae (Ascomycota, Diaporthales)

“…Macrofungi have been widely applied for biogeographical analyses [ 24 , 48 , 49 , 50 , 51 ]. Our study suggested that the species distribution and speciation of Pseudoplagiostomataceae had a particular biogeographical pattern, and these species appeared to originate in Asia, particularly in Southeast Asia.…”

“…Genomic DNA was extracted from fungal mycelia grown on PDA, using a kit (OGPLF-400, GeneOnBio Corporation, Changchun, China) according to the manufacturer’s protocol [ 24 ]. Gene sequences were obtained from five loci including the internal transcribed spacer regions with the intervening 5.8S nrRNA gene (ITS), the partial large subunit nrRNA gene (LSU), the partial DNA-directed RNA polymerase II subunit two gene ( rpb2 ), the partial translation elongation factor 1-alpha gene ( tef1α ), and the partial beta-tubulin gene ( tub2 ) were amplified by the primer pairs and polymerase chain reaction (PCR) programs listed in Table 1 .…”

Two new species of Haploporus (Polyporales, Basidiomycota) from China and Ecuador based on morphology and phylogeny

“…The internal transcribed spacers (ITS), large subunit of nuclear ribosomal RNA gene (LSU), and small subunit mitochondrial rRNA gene (mtSSU) were amplified with primer pairs ITS 5 (5′‐GGA AGT AAA AGT CGT AAC AAG G‐3′) and ITS 4 (5′‐TCC TCC GCT TAT TGATAT GC‐3′; White et al., 1990 ), LR0R (5′‐ACC CGC TGA ACT TAA GC‐3′) and LR7 (5′‐TAC TAC CAC CAA GAT CT‐3′; ), and MS1 (5′‐CAG CAG TCA AGA ATA TTA GTC AAT G‐3′) and MS2 5′‐GCG GAT TAT CGA ATT AAA TAA C‐3′; White et al., 1990 ), respectively. The PCR procedures were as follows: for ITS and mtSSU regions, an initial denaturation at 95°C for 3 min, followed by 34 cycles at 94°C for 40 s, 54°C for ITS and 55°C for mtSSU for 45 s and 72°C for 1 min, and a final extension of 72°C for 10 min; for the LSU region, an initial denaturation at 94°C for 1 min, followed by 34 cycles at 94°C for 30 s, 50°C for 1 min and 72°C for 1.5 min, and a final extension of 72°C for 10 min ( Zhou et al., 2021 ; Zhao et al., 2022c ). The PCR products were sequenced using BGI Tech Solutions (Beijing Liuhe Co., Ltd., Beijing, China).…”

“…biology.duke.edu/fungi/mycolab/primers.htm ), and MS1 (5′-CAG CAG TCA AGA ATA TTA GTC AAT G-3′) and MS2 5′-GCG GAT TAT CGA ATT AAA TAA C-3′; White et al, 1990), respectively. The PCR procedures were as follows: for ITS and mtSSU regions, an initial denaturation at 95°C for 3 min, followed by 34 cycles at 94°C for 40 s, 54°C for ITS and 55°C for mtSSU for 45 s and 72°C for 1 min, and a final extension of 72°C for 10 min; for the LSU region, an initial denaturation at 94°C for 1 min, followed by 34 cycles at 94°C for 30 s, 50°C for 1 min and 72°C for 1.5 min, and a final extension of 72°C for 10 min (Zhou et al, 2021;Zhao et al, 2022c). The PCR products were sequenced using BGI Tech Solutions (Beijing Liuhe Co., Ltd., Beijing, China).…”

Association of Onnia subtriquetra with living and dead bishop pine (Pinus muricata) and shore pine (Pinus contorta var. contorta) in California, USA

“…Onnia species are distributed primarily in the northern hemisphere and are known for parasitizing gymnosperms. Relatively recent work established six well-supported species of Onnia in Europe, Asia and North America (Ji et al, 2017), with a seventh added more recently (Zhao et al, 2022). Among these species, Onnia tomentosa and O. leporina had occurrence records in North America before the publication of the generic revision of Ji et al (2017) (Global Biodiversity Information Facility, 2023).…”