ABSTRACT
The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.
ABSTRACT
The Russian Far East (RFE) is an important hotspot of biodiversity whose insect fauna remains understudied, particularly its Microlepidoptera. Here we explore the diversity of leaf-mining micromoths of the family Gracillariidae, their distribution and host plant associations in RFE using a combination of field observations and sampling, DNA barcoding, morphological analysis and literature review. We collected 91 gracillariid specimens (45 larvae, 9 pupae and 37 adults) in 12 localities across RFE and identified 34 species using a combination of DNA barcoding and morphology. We provide a genetic library of 57 DNA barcodes belonging to 37 Barcode Index Numbers (BINs), including four BINs that could potentially represent species new to science. Leaf mines and leaf shelters are described and illustrated for 32 studied species, male or female genitalia as well as forewing patterns of adults are shown, especially for those species identified based on morphology. Three species, Micrurapteryx caraganella (Hering), Callisto insperatella (Nickerl), and Phyllonorycter junoniella (Zeller) are newly recorded from RFE. Five species previously known from some regions of RFE, were found for the first time in Amurskaya Oblast: Phyllonorycter populifoliella (Treitschke), Primorskii Krai: Ph. sorbicola Kumata and Sahkalin Island: Caloptilia heringi Kumata, Ph. ermani (Kumata) and Ph. ulmifoliella (Hübner). Eight gracillariid-plant associations are novel to science: Caloptilia gloriosa Kumata on Acer pseudosieboldianum, Cameraria niphonica Kumata on A. caudatum subsp. ukurundense, Parornix ermolaevi Kuznetzov on Corylus sieboldiana, Phyllonorycter ermani (Kumata) on Betula platyphylla, Ph. nipponicella (Issiki) on Quercus mongolica, Ph. orientalis (Kumata) and Ph. pseudojezoniella Noreika on Acer saccharum, Ph. sorbicola on Prunus maakii. For the first time we documented the "green island" phenotype on Phyllonorycter cavella (Zeller) mines on Betula platyphylla. Two pestiferous species have been recorded during our surveys: Micrurapteryx caraganella on ornamental Caragana arborescens in urban plantations in Amurskaya Oblast, and the lime leafminer Phyllonorycter issikii (Kumata), a species known to be native to RFE and invasive elsewhere in Russia and in European countries. A revised checklist of RFE gracillariids has been compiled. It accounts for 135 species among which 17 species (13%) are only known to occur in RFE. The gracillariid fauna of RFE is more similar to the Japanese fauna (49%), than to the fauna of the rest of Russia (i.e European part and Siberia) (32%).
