Phyllachora species infecting maize and other grass species throughout the Americas represents a complex of closely related species which vary in their host and geographic range

The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905-2019. These 186 isolates were grouped into 5 distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium species, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were identified based on morphology and host association, but our sequence data indicates some Phyllachora species are capable of infecting a broad range of host species and there may be significant synonymy in the Phyllachora genus and additional work on species delineation and host specificity should be considered.

Molecular phylogeny and diversity of Laburnicola (Didymosphaeriaceae): a new species from Uzbekistan

Laburnicola is a genus in Didymosphaeriaceae that includes saprobic and endophytic fungal taxa. The current study conducted in the subalpine region of Uzbekistan discovered a new species on a dead stem of a wild rose plant. Maximum likelihood and Bayesian analyses of combined LSU, SSU, ITS, and TEF 1-ɑ dataset confirmed the new species’ taxonomic position in Laburnicola. Our new species, Laburnicola zaaminensis (TASM 6152), was clustered with L. dactylidis (MFLUCC 16-0285) with strong bootstrap support. A detailed description together with illustrations are provided for Laburnicola zaaminensis. Furthermore, an annotated species list, a distribution map, and a taxonomic key for Laburnicola species are provided. This is the first record of Laburnicola from Central Asia.

Two new species and one new record of Hyalopsora (Pucciniastraceae) on ferns in China

Three rust fungi belonging to the genus Hyalopsora occurring on ferns were found in China. Hyalopsora minispora and H. tibetica are described as new species in this paper. Hyalopsora minispora can be distinguished from known species by its relatively small urediniospores (19.5–23.0 × 12.0–19.0 μm) with 4–6 scattered germ pores and amphispores in a common pustule. Hyalopsora tibetica is mainly characterized by urediniospores with 2–6 scattered germ pores and amphispores. Hyalopsora neocheilanthis is described and reported as a new record for China. The phylogenetic relationships of Hyalopsora species and related taxa were examined by comparing the sequences of their internal transcribed spacer 2 (ITS2) barcode and 28S rDNA gene segments. Hyalopsora is supported with strong bootstrap support and it differs from the two other fern-infecting genera viz. Milesina and Uredinopsis.

Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia

Broomcorn millet (Panicum miliaceum L.) was domesticated in northern China at least 7,000 years ago and was subsequentially adopted as a cereal in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, a region that has an important history in crop domestication. The rich botanical material found at Areni-1 includes grains identified by morphology as broomcorn millet that were 14C dated to the medieval era (873 ± 36 CE and 1118 ± 35 CE). To retrace the demographic history of these broomcorn millet samples, we used ancient DNA extraction and hybridization capture enrichment to sequence and assemble three chloroplast genomes from the Areni-1 grains and then compared these sequences to 50 modern chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity and little inference on broomcorn demography could be made. However, in a phylogeny the chloroplast genomes separated into two clades with strong bootstrap support, similar to what has been reported for nuclear DNA from broomcorn millet. In a haplotype network, the chloroplast genomes of two accessions of wild (undomesticated) broomcorn millet contained a relatively large number of variants, 11 SNPs. These SNPs were not present in the domesticated varieties, suggesting these wild accessions may not be directly related to the lineages that underwent domestication or that broomcorn millet may have undergone a domestication bottleneck resulting in lost diversity in the chloroplast genome. These results demonstrate that broomcorn millet from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

The complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

Comparative Analysis of Complete Chloroplast Genome Sequences in Edgeworthia (Thymelaeaceae) and New Insights Into Phylogenetic Relationships

The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora, Edgeworthia chrysantha, and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndhF to the trnL-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia, further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia.

Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, Danxiaorchis singchiana, Reveals Heavy Gene Loss and Gene Relocations

Danxiaorchis singchiana (Orchidaceae) is a leafless mycoheterotrophic orchid in the subfamily Epidendroideae. We sequenced the complete plastome of D. singchiana. The plastome has a reduced size of 87,931 bp, which includes a pair of inverted repeat (IR) regions of 13,762 bp each that are separated by a large single copy (LSC) region of 42,575 bp and a small single copy (SSC) region of 17,831 bp. When compared to its sister taxa, Cremastra appendiculata and Corallorhiza striata var. involuta, D. singchiana showed an inverted gene block in the LSC and SSC regions. A total of 61 genes were predicted, including 21 tRNA, 4 rRNA, and 36 protein-coding genes. While most of the housekeeping genes were still intact and seem to be protein-coding, only four photosynthesis-related genes appeared presumably intact. The majority of the presumably intact protein-coding genes seem to have undergone purifying selection (dN/dS < 1), and only the psaC gene was positively selected (dN/dS > 1) when compared to that in Cr. appendiculata. Phylogenetic analysis of 26 complete plastome sequences from 24 species of the tribe Epidendreae had revealed that D. singchiana diverged after Cr. appendiculata and is sister to the genus Corallorhiza with strong bootstrap support (100%).

Defining new dung beetle tribes to resolve discrepancies between phylogeny and tribal classification in the subfamily Scarabaeinae (Coleoptera: Scarabaeidae)

The monophyletic, dung beetle subfamily, Scarabaeinae, has a long history of subdivision into tribes and subtribes represented by groups of genera unified by designated characters. Various tribal names have been proposed although only 11 or 12 were considered valid in recent reviews. Three of these 12 tribes have now been invalidated due to extensive polyphyly indicated by both morphological and molecular phylogenies. Although partial revision of tribal classification was proposed in the most recent global molecular phylogeny of the subfamily, this was primarily limited to redefinition of membership or provision of support for pre-existing tribes. Complete revision was not attempted as the phylogeny examined interrelationships between only ~52% of the valid described genera. It was also hampered by inconsistencies in topology using different analytical methods, weakened by limited bootstrap support for many basal nodes, as well predicting several phylogenetic relationships that seemed anomalous with regards to biogeographical hypotheses. Nevertheless, using this phylogeny, we propose further revision of tribal classification in a clade of primarily African genera included within a group defined as “basal Scarabaeinae”. Using three different methods, the sister lineages of this clade were consistently recovered, mostly with strong bootstrap support for their molecular relatedness. Therefore, we provide a number of defining morphological characters to support their proposed designation as three new tribes: Byrrhidiini, Endroedyolini and Odontolomini. We also discuss approaches to a full tribal revision as well as the implications for historical biogeography of the Scarabaeinae.

Molecular taxonomy reveals the sexual morph of Nodulosphaeria digitalis in Phaeosphaeriaceae from Campanula trachelium in Italy

The fungal genus Nodulosphaeria is one of the oldest phaeosphaeriaceous genera that comprises saprobic, endophytic and pathogenic species associated with a wide variety of substrates. There are 71 species epithets listed under Nodulosphaeria in Index Fungorum and most of these published records lack illustrations and descriptions, or DNA sequence data and thus it is challenging to confirm their names or investigate taxonomic relationships. In this study, we report the sexual morph of Nodulosphaeria digitalis, a terrestrial saprobe belonging to the genus Nodulosphaeria (Phaeosphaeriaceae, Pleosporales), on stems of Campanula trachelium from Arezzo Province, Italy. This is the first record of a Nodulosphaeria taxon on Campanulaceae. Maximum likelihood, Maximum parsimony and Bayesian inference analyses of combined ITS, LSU, SSU and TEF1-α sequence data reveal that the novel isolate belongs to the family Phaeosphaeriaceae and nests with Nodulosphaeria digitalis with strong bootstrap support. The detailed descriptions and illustrations of the sexual morph of N. digitalis, an updated phylogenetic tree for the genus Nodulosphaeria are provided.

A Wildlife Forensic Study for the Species Identification of Indian Blackbuck through Forensically Informative Nucleotide Sequencing (FINS)

Identification of exhibits obtained in wildlife cases usually presents challenging tasks for the forensic science investigators. This study describes a casework, where a degraded tissue sample was recovered from pathology department LUVAS University Hisar, Haryana to resolve the identity of the questioned sample. The mitochondrial DNA region of the questioned sample was amplified and sequenced using universal primers of cytochrome b gene to determine the forensically informative nucleotide sites to find the species identity. The obtained sequencing results were compared with the most homologous sequences extracting from NCBI-GenBank database and a phylogenetic tree was done with the aligned sequences to determine the species identity with strong bootstrap support. The informative sites generated revealed that the degree of sequence similarity showed maximum homology (100%) with the sequence obtained from the database. Based on the FINS analysis the recovered sample related to Antilope cervicapra (family Bovidae).