Avocado is one of the most important crops in the world, and Mexico is the largest producer of this fruit. Several insect pests affect its production, and thrips are amongst the most important. A key step in the desig...Avocado is one of the most important crops in the world, and Mexico is the largest producer of this fruit. Several insect pests affect its production, and thrips are amongst the most important. A key step in the design of control methods is accurate species identification. Despite this, formal reports on species diversity of thrips in Mexico are very scarce. Morphological identification can sometimes be time-consuming and inconclusive. Therefore, we explored the species diversity of thrips in Mexican avocado orchards （Michoacan state） based on partial sequences of the mitochondrial gene cytochrome oxidase subunit I （COl）. Forty-four specimens were analysed, which represented approximately 8% of all individuals collected from five localities distributed in three Municipalities. All specimens were analysed using the COl marker, and specimens within the genera Frankliniella were also analysed using a marker within the D2 domain of the 28S （28SD2） nuclear ribosomal DNA. Molecular identifications were confirmed using morphological taxonomy. Overall, six genera were found （Neohydatothrips, Scirtothrips, Frankliniella, Arorathrips, Caliothrips and Leptothrips）. AII genera contained only one species, except Frankliniella, for which there were six species. Data from the two molecular markers suggest the existence of cryptic species within Mexican F. occidentalis populations.展开更多
The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa,has dramatically changed the classification system of early-diverging fungi over the past sev...The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa,has dramatically changed the classification system of early-diverging fungi over the past several decades.The number of phyla established for non-Dikarya fungi has increased from 2 to 17.However,to date,both the classification and phylogeny of the basal fungi are still unresolved.In this article,we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla.We also provide information on the ecology and distribu-tion in Mucoromycota and highlight the impact of chytrids on amphibian populations.Species concepts in Chytridiomycota,Aphelidiomycota,Rozellomycota,Neocallimastigomycota are discussed in this paper.To preserve the current application of the genus Nephridiophaga(Chytridiomycota:Nephridiophagales),a new type species,Nephridiophaga blattellae,is proposed.展开更多
Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cann...Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases.展开更多
基金scholarship from Consejo Nacional de Ciencia y Tenología (CONACyT), Mexico
文摘Avocado is one of the most important crops in the world, and Mexico is the largest producer of this fruit. Several insect pests affect its production, and thrips are amongst the most important. A key step in the design of control methods is accurate species identification. Despite this, formal reports on species diversity of thrips in Mexico are very scarce. Morphological identification can sometimes be time-consuming and inconclusive. Therefore, we explored the species diversity of thrips in Mexican avocado orchards （Michoacan state） based on partial sequences of the mitochondrial gene cytochrome oxidase subunit I （COl）. Forty-four specimens were analysed, which represented approximately 8% of all individuals collected from five localities distributed in three Municipalities. All specimens were analysed using the COl marker, and specimens within the genera Frankliniella were also analysed using a marker within the D2 domain of the 28S （28SD2） nuclear ribosomal DNA. Molecular identifications were confirmed using morphological taxonomy. Overall, six genera were found （Neohydatothrips, Scirtothrips, Frankliniella, Arorathrips, Caliothrips and Leptothrips）. AII genera contained only one species, except Frankliniella, for which there were six species. Data from the two molecular markers suggest the existence of cryptic species within Mexican F. occidentalis populations.
基金HBL was supported by the Graduate Program for the Undiscovered Taxa of Korea(NIBR202130202)by the Project on Survey and Discovery of Indigenous Fungal Species of Korea funded by NIBR+8 种基金by the Project on Discovery of Fungi from Freshwater and Collection of Fungarium funded by NNIBR of the Ministry of Environment(MOE)of the Republic of KoreaTYJ and DRS were supported by the US National Science Foundation Grants tDBI-1756202,DBI-1910720,and DEB-1929738GHJ thank FAPESP(2018/24915-1 and 2019/17237-0)KS was supported by a Grant-in-Aid for JSPS Overseas Research Fellowship from the Japan Society for the Promotion of ScienceBW was supported by grants from the National Research Foundation of Korea funded by the Ministry of Education(2015R1D1A01057282)the Ministry of Science,ICT,and Future Planning(2018R1A2B6006833)of the Republic of KoreaALS was supported by the Fundação de AmparoàCiência do Estado de Perbambuco and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior(FACEPE/CNPq-APQ-0842-2.12/14.)We thank the National Council for Scientific and Technological Development(CNPq)for the research scholarship Granted to ALS.RR and JFHS were supported by Grants of the German Research Foundation(DFG,RA850/6-1 Project No.397619173 and STR1349/2-1 Project No.432453260,respectively)KV was supported by the German Research Foundation(DFG)through the Collaborative Research Center/Transregio FungiNet 124‘Pathogenic fungi and their human host:Networks of Interaction’,DFG Project Number 210879364,Project A6.
文摘The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa,has dramatically changed the classification system of early-diverging fungi over the past several decades.The number of phyla established for non-Dikarya fungi has increased from 2 to 17.However,to date,both the classification and phylogeny of the basal fungi are still unresolved.In this article,we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla.We also provide information on the ecology and distribu-tion in Mucoromycota and highlight the impact of chytrids on amphibian populations.Species concepts in Chytridiomycota,Aphelidiomycota,Rozellomycota,Neocallimastigomycota are discussed in this paper.To preserve the current application of the genus Nephridiophaga(Chytridiomycota:Nephridiophagales),a new type species,Nephridiophaga blattellae,is proposed.
基金funded by the Estonian Science Foundation(Grants PUT1399,PRG632,MOBERC21)。
文摘Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases.
