Phylogeny of Ptychostomum (Bryaceae,Musci) inferred from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) and chloroplast rps4

The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.

Genetic variation and phylogenetic relationship of Hypoderaeum conoideum(Bloch, 1782) Dietz, 1909(Trematoda: Echinostomatidae) inferred from nuclear and mitochondrial DNA sequences

Objective:To explore genetic variations of Hypoderaeum conoideum collected from domestic ducks from 12 different localities in Thailand and Lao PDR,as well as their phylogenetic relationship with American and European isolates.Methods:The nucleotide sequences of their nuclear ribosomal DNA(ITS),mitochondrial cytochrome c oxidase subunit 1(CO1),and NADH dehydrogenase subunit 1(ND1)were used to analyze genetic diversity indices.Results:We found relatively high levels of nucleotide polymorphism in ND1(4.02%),whereas moderate and low levels were observed in CO1(2.11%)and ITS(0.96%),respectively.Based on these polymorphisms,the 20 ND1,12 CO1,and 18 ITS haplotypes were classified,and several common haplotypes were observed in all samples.At least three major lineages,namely American,European and Asian lineages,have been classified by phylogenetic analyses based on ND1 sequences.Conclusions:Our report demonstrates that the ND1 gene is the most suitable genetic marker to explore genetic variation and phylogenetic relationship of Hypoderaeum conoideum.However,a combination of all loci for ND1,CO1 and ITS would be of great value toward further genetic investigation of this endemic worldwide parasite.Thus,comprehensive molecular genetic analyses of Hypoderaeum conoideum from its worldwide distribution is needed to further understanding of the evolutionary and systematic relationships of this parasite.

Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop improvement.We produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 B.oleracea breeding lines.We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major repeats.Nuclear genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 accessions.Interestingly,some SNPs showed subspecies enrichment at certain chromosomal regions.The assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and indels.The 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 lines.The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another group.The morphotypes diverged during the last 0.17 million years.The Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead.The polymorphic Cp markers provide a classification system for the cytoplasm types in B.oleracea.Furthermore,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active recently.Overall,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B.oleracea morphotypes.

Species diversity of thrips (Thysanoptera) in selected avocado orchards from Mexico based on morphology and molecular data

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.

Phylogeny and Biogeography of Thuja L. （Cupressaceae）, an Eastern Asian and North American Disjunct Genus

In order to develop better insights into biogeographic patterns of eastern Asian and North American disjunct plant genera, sequences of nuclear ribosomal DNA internal transcribed spacer (nr DNA ITS) region were used to estimate interspecific relationships of Thuja L. (Cupressaceae) and infer its biogeography based on the phylogeny. According to the phylogenetic analysis, two clades were recognized. The first clade included Thuja plicata D. Don (western North America) and T. koraiensis Nakai (northeastern Asia), and the second one contained T. occidentalis(Gord.) Carr. (Japan). The ancestral area of Thuja was inferred to be eastern Asia, and two dispersal events were responsible for the modern distribution of Thuja in North America. Both the North Atlantic land bridge and Bering land bridge were possible routes for the migration of ancestral populations to North America.

The unbearable lightness of sequenced-based identification

Using the basic GenBank local alignment search tool program(BLAST)to identify fungi collected in a recently protected beech forest at Montricher(Switzerland),the number of ITS sequences associated to the wrong taxon name appears to be around 30%,even higher than previously estimated.Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected,viz.first records for Switzerland,rare or patrimonial species and problematic species(when BLAST top scores were equally high for different species),all belonging to Agaricomycotina.This paper dissects for the first time a number of sequence-based identifications,thereby showing in every detail—particularly to the user community of taxonomic information—why sequence-based identification in the context of a fungal inventory can easily go wrong.Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories:we spent two months on verification of approx.20 identifications.Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification,it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata.While checking the original publications associated with top score sequences for the few examples that were here re-examined,a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank.Advantages and pitfalls of sequence-based identification are discussed,particularly in the light of undertaking fungal inventories.Recommendations are made to avoid or reduce some of the major problems with sequence-based identification.Nevertheless,the prospects for a more reliable sequence-based identification of fungi remain quite dim,unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.