Plastid genome evolution of a monophyletic group in the subtribe Lauriineae(Laureae,Lauraceae)

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.

Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae

All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life.However,the phylogenomic relationships among its three subfamilies(Myospalacinae,Spalacinae,and Rhizomyinae)and the molecular basis underlying their adaptations to underground life remain poorly understood.Here,we inferred the phylogenomic relationships among these subfamilies based on de novo sequencing the genome of the hoary bamboo rat(Rhizomys pruinosus).Analyses showed that 50%of the identified 11028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae.

Fungal diversity notes 929-1035:taxonomic and phylogenetic contributions on genera and species of fungi

This article is the ninth in the series of Fungal Diversity Notes,where 107 taxa distributed in three phyla,nine classes,31 orders and 57 families are described and illustrated.Taxa described in the present study include 12 new genera,74 new species,three new combinations,two reference specimens,a re-circumscription of the epitype,and 15 records of sexualasexual morph connections,new hosts and new geographical distributions.Twelve new genera comprise Brunneofusispora,Brunneomurispora,Liua,Lonicericola,Neoeutypella,Paratrimmatostroma,Parazalerion,Proliferophorum,Pseudoastrosphaeriellopsis,Septomelanconiella,Velebitea and Vicosamyces.Seventy-four new species are Agaricus memnonius,A.langensis,Aleurodiscus patagonicus,Amanita flavoalba,A.subtropicana,Amphisphaeria mangrovei,Baorangia major,Bartalinia kunmingensis,Brunneofusispora sinensis,Brunneomurispora lonicerae,Capronia camelliaeyunnanensis,Clavulina thindii,Coniochaeta simbalensis,Conlarium thailandense,Coprinus trigonosporus,Liua muriformis,Cyphellophora filicis,Cytospora ulmicola,Dacrymyces invisibilis,Dictyocheirospora metroxylonis,Distoseptispora thysanolaenae,Emericellopsis koreana,Galiicola baoshanensis,Hygrocybe lucida,Hypoxylon teeravasati,Hyweljonesia indica,Keissleriella caraganae,Lactarius olivaceopallidus,Lactifluus midnapurensis,Lembosia brigadeirensis,Leptosphaeria urticae,Lonicericola hyaloseptispora,Lophiotrema mucilaginosis,Marasmiellus bicoloripes,Marasmius indojasminodorus,Micropeltis phetchaburiensis,Mucor orantomantidis,Murilentithecium lonicerae,Neobambusicola brunnea,Neoeutypella baoshanensis,Neoroussoella heveae,Neosetophoma lonicerae,Ophiobolus malleolus,Parabambusicola thysanolaenae,Paratrimmatostroma kunmingensis,Parazalerion indica,Penicillium dokdoense,Peroneutypa mangrovei,Phaeosphaeria cycadis,Phanerochaete australosanguinea,Plectosphaerella kunmingensis,Plenodomus artemisiae,P.lijiangensis,Proliferophorum thailandicum,Pseudoastrosphaeriellopsis kaveriana,Pseudohelicomyces menglunicus,Pseudoplagiostoma mangiferae,Robillarda mangiferae,Roussoella elaeicola,Russula choptae,R.uttarakhandia,Septomelanconiella thailandica,Spencermartinsia acericola,Sphaerellopsis isthmospora,Thozetella lithocarpi,Trechispora echinospora,Tremellochaete atlantica,Trichoderma koreanum,T.pinicola,T.rugulosum,Velebitea chrysotexta,Vicosamyces venturisporus,Wojnowiciella kunmingensis and Zopfiella indica.Three new combinations are Baorangia rufomaculata,Lanmaoa pallidorosea and Wojnowiciella rosicola.The reference specimens of Canalisporium kenyense and Tamsiniella labiosa are designated.The epitype of Sarcopeziza sicula is re-circumscribed based on cyto-and histochemical analyses.The sexual-asexual morph connection of Plenodomus sinensis is reported from ferns and Cirsium for the first time.In addition,the new host records and country records are Amanita altipes,A.melleialba,Amarenomyces dactylidis,Chaetosphaeria panamensis,Coniella vitis,Coprinopsis kubickae,Dothiorella sarmentorum,Leptobacillium leptobactrum var.calidus,Muyocopron lithocarpi,Neoroussoella solani,Periconia cortaderiae,Phragmocamarosporium hederae,Sphaerellopsis paraphysata and Sphaeropsis eucalypticola.

Forecasting the number of species of asexually reproducing fungi(Ascomycota and Basidiomycota)

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions.A large number of such taxa are among the most notorious plant and animal pathogens.In addition,they have a key role in food production,biotechnology and medicine.Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy.The number,variation and diversity of asexually reproducing taxa are insufficiently known,even though fungi capable of asexual reproduction may provide an untapped,rich biological resource for future exploitation.Currently,ca.30,000 asexual species belonging to ca.3800 genera have been reported(including 1388 coelomycetous and 2265 hyphomycetous genera).Recent reports(2017–2020)reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi.With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi,priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa.However,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed.The number of species of speciose genera(e.g.Alternaria,Aspergillus,Cercospora,Fusarium,Phoma and Pseudocercospora),cryptic species,species of pleomorphic genera,less studied life modes(such as lichenicolous taxa,taxa from extreme environments)and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity.This paper discusses the current knowledge on the matter,with diversity estimates,and potential obstacles in several chapters on(1)speciose genera;(2)pleomorphic genera;(3)cryptic species;(4)well-studied but insufficiently resolved taxa,e.g.leaf inhabiting species,marine fungi,(5)less studied life modes,e.g.lichenicolous,rock-inhabiting fungi,insect-associated and yeast-forming taxa and(6)species from biodiversity-rich areas.