Litsea, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of Litsea taxa. One is composed of 16 Litsea taxa and two Lindera taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.

The family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences. The mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present. The topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day.

Shiraiaceae is an important family in Pleosporales (Dothideomycetes), which includes medical fungi and plant pathogens. Two hypocrellin-producing taxa, Shiraia bambusicola and a novel genus Rubroshiraiagen. nov., typified by Rubroshiraia bambusae are treated in this article. Maximum likelihood analysis, generated via RAxML (GTR+G model), using a combined SSU, LSU, TEF1 and RPB2 sequence dataset, shows that Rubroshiraia is close to Shiraia and belongs to the family Shiraiaceae. Descriptions, illustrations and a taxonomic key are provided for the genera in Shiraiaceae. Rubroshiraia morphologically differs from Shiraia in having small and dark ascostromata and filiform ascospores. Production of the ascostromatal metabolites, hypocrellin A and B, were examined by HPLC and spectrophotometer. The content of hypocrellin A and B of specimen HKAS 102255 (R. bambusae) is twice that produced by HKAS 102253 (S. bambusicola). To clarify the relationship between R. bambusae and Hypocrella bambusae, type material of the latter was examined and provided the illustration.

Morphological comparisons and multi locus phylogenetic analyses (base on the combined genes of ITS, LSU, rpb2 and tub) demonstrated that three new saprobic taxa isolated from bamboo belong to Cainiaceae. These taxa comprise a novel genus Paramphibambusa (P. bambusicolasp. nov.) and two new species, Arecophila xishuangbannaensis and A. zhaotongensis. The three new taxa belong to Cainiaceae (Xylariales, Sordariomycetes) a poorly studied family, which now comprises eight genera. Paramphibambusa can be distinguished from other Cainiaceae genera in having ascomata with a neck and ascospores lacking longitudinal striation, germ slits or germ pores. The two new Arecophila species clustered in a clade with Arecophila sp. and A. bambusae. Detailed morphological descriptions, illustrations, and an updated phylogenetic tree are provided for the new taxa.

The evolution of a species can be understood in the context of two major concepts—the cryptic species concept and the phenotypic noise concept. The former represents morphologically indistinguishable but genetically distinct evolutionary lineages, while the latter represents the phenotypic variations of an isogenic population. Although the concept of cryptic species currently represents a general topic, its effect on other aspects of biology, such as biodiversity, ecology, evolutionary biology, and taxonomy, is still unclear. In particular, cryptic species cause complications and prevent the development of a clear taxonomy. The phenotypic noise concept or phenotypic plasticity generally refers to the various expressions of phenotypes in different environments. Hence, the cryptic species concept refers to genetic variations, while the phenotypic noises concept is about non-genetic variations. Although both concepts are opposites, they each contribute significantly to the evolutionary process of an organism. Despite the extensive research studies and publications discussing those two concepts in separate accounts, a concise account that combines and compares both concepts are generally lacking. Nevertheless, these are essential to understand the evolutionary process clearly. This review addresses the available literature on this topic, intending to provide a general and overall discussion on both the cryptic species concept and the phenotypic noise concept and their effect on evolution, ecology, biodiversity, and taxonomy with a special focus on fungal systematics. hence, several fungal case studies representing the two concepts are presented, compared, and discussed for a better understanding.

The genus Strobilomyces, representing a diverse and widespread group of ectomycorrhizal mushroom-forming fungi, plays a crucial ecological and economical role. However, until now, a comprehensive description of its mitochondrial genome (mitogenome) has been lacking. In our current study, we have successfully assembled and analysed the mitogenomes of five Strobilomyces species. These mitogenomes span a range from 35,618 base pairs (bp) to 42,088 bp, exhibiting a higher nucleotide abundance of AT compared to GC. All five mitogenomes harbour 14 conserved protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and 24 transfer RNAs (tRNAs). Notably, the overall ratio of Ka/Ks for all PCGs was found to be less than 1.0, indicating that these genes have undergone purifying selection during evolution. Intriguingly, the mitogenomic comparison revealed two instances of gene re-arrangement, which were directly linked to the geographical distribution of the Strobilomyces species. The concatenated mitochondrial PCGs (mtPCGs) and nuclear ribosomal DNA (nrDNA) phylogenies displayed a robust congruent topology at the family level. Specifically, the Strobilomyces species clustered together and formed sister relationship with other Boletaceae species in the mtPCGs tree. In contrast, the Strobilomyces species grouped at the base of the nrDNA tree when concerning Boletaceae. This study represents the first report on the mitogenomes of the Strobilomyces genus, providing valuable insights into fungal evolution within Boletales.