Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

Phylogenetic and molecular clock analyses were performed including all genera except one (Pseudomonotes) for the three subfamilies of Dipterocarpaceae. We also included representatives of Sarcolaenaceae and Cistaceae with Bixaceae as the ultimate outgroup. Three plastid regions (six markers), partial rbcL, trnK-matK-trnK (partial trnK intron including complete matK) and trnT-trnL-trnF (partial trnT, complete trnT-trnL intergenic spacer, complete trnL, complete trnL-trnF intergenic spacer and partial trnF), were analysed. We also investigated additional accessions for genome size and chromosome numbers. Our phylogenetic results differ in three important respects from previous interpretations of morphological characters, as reflected in recent classifications. First, our analyses strongly support assignment of Pakaraimaea (subfamily Pakaraimaeoideae) to Cistaceae. Second, the morphological concepts of Dipterocarpeae and Shoreeae in subfamily Dipterocarpoideae are not supported because Dipterocarpus is sister to Dryobalanops plus tribe Shoreeae. Our analysis revealed four clades: (1) Dipterocarpus; (2) Dryobalanops, for which tribal assignment has been contentious; (3) genera of Shoreeae; and (4) the remaining genera of Dipterocarpeae. Third, Shorea is not monophyletic. Monotoideae are weakly supported as sister to Dipterocarpoideae; Sarcolaenaceae (endemic to Madagascar) are sister to this pair. Divergence in extant Dipterocarpoideae occurred c. 55 Mya. Genome sizes for all accessions examined are small (0.3264–0.6724 pg), and the additional chromosome numbers we collected fit into the patterns previously observed for Dipterocarpaceae.

Premise of the study: PCR amplification of the matK barcoding region is often difficult when dealing with multiple angiosperm families. We developed a primer cocktail to amplify this region efficiently across angiosperm diversity.Methods and Results: We developed 14 matK primers (seven forward, seven reverse) for multiplex PCR, using sequences available in GenBank for 178 taxa belonging to 123 genera in 41 families and 18 orders. Universality of these new multiplexed primers was tested with 53 specimens from 44 representative angiosperm families in 23 different orders. Our primers showed high PCR amplification and sequencing success.Conclusions: These results show that our newly developed primers are highly effective for multiplex PCR and can be employed in future barcode projects involving taxonomically diverse samples across angiosperms. Using multiplex primers for barcoding will reduce the cost and time needed for PCR amplification.

Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

Gentiana is a sub‐cosmopolitan temperate genus among the most species‐rich in Gentianaceae. Although molecular data (produced via Sanger sequencing) allowed the resolution of phylogenetic relationships between Gentiana and other genera in subtribe Gentianinae, the validity of sections within the genus remains largely untested. In this study, we evaluated the monophyly of all 14 sections attributed to Gentiana, using 294 unlinked anchored loci, the nuclear ribosomal DNA (rDNA) cistron as well as plastid genomes, all produced by anchored hybrid enrichment. We reconstructed phylogenetic relationships by conducting maximum likelihood and Bayesian analyses. These analyses represent a significant improvement over previous taxonomic studies using molecular tools. Our results partly correspond to traditional taxonomic treatments, with several sections being well supported as monophyletic, including Gentiana sect. Calathianae, sect. Ciminalis, sect. Cruciata, sect. Frigida, sect. Gentiana and sect. Pneumonanthe. In contrast, G. sect. Isomeria, sect. Microsperma and sect. Monopodiae were found to be polyphyletic, whereas sect. Dolichocarpa and sect. Fimbricorona were nested within sect. Chondrophyllae. We here provide new taxonomic treatments for these sections, mostly based upon the traditional delineation of their series, which were recovered as monophyletic. In our new treatment, Gentiana encompasses 13 sections. A new determination key to the sections of Gentiana is provided.

Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.