A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164\ua0Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models

The Genomics and Population Genomics of the Light Brown Apple Moth, Epiphyas postvittana, an Invasive Tortricid Pest of Horticulture

The light brown apple moth, Epiphyas postvittana is an invasive, polyphagous pest of horticultural systems around the world. With origins in Australia, the pest has subsequently spread to New Zealand, Hawaii, California and Europe, where it has been found on over 500 plants, including many horticultural crops. We have produced a genomic resource, to understand the biological basis of the polyphagous and invasive nature of this and other lepidopteran pests. The assembled genome sequence encompassed 598 Mb and has an N50 of 301.17 kb, with a BUSCO completion rate of 97.9%. Epiphyas postvittana has 34% of its assembled genome represented as repetitive sequences, with the majority of the known elements made up of longer DNA transposable elements (14.07 Mb) and retrotransposons (LINE 17.83 Mb). Of the 31,389 predicted genes, 28,714 (91.5%) were assigned to 11,438 orthogroups across the Lepidoptera, of which 945 were specific to E. postvittana. Twenty gene families showed significant expansions in E. postvittana, including some likely to have a role in its pest status, such as cytochrome p450s, glutathione-S-transferases and UDP-glucuronosyltransferases. Finally, using a RAD-tag approach, we investigated the population genomics of this pest, looking at its likely patterns of invasion

Odorant Receptors of the New Zealand Endemic Leafroller Moth Species Planotortrix octo and P. excessana.

Moths use their sense of smell to find food sources, mating partners and oviposition sites. For this they possess a family of odorant receptors (ORs). Some ORs are used by both sexes whereas others have sex-specific roles. For example, male moths possess ORs specifically tuned to sex pheromones produced by conspecific females. Here we identify sets of ORs from the antennae of New Zealand endemic leafroller moths Planotortrix octo (48 ORs) and P. excessana (47 ORs) using an RNA-Seq approach. Two orthologous ORs show male-biased expression in the adult antennae of both species (OR7 and OR30) and one other OR in each species was female-biased in its expression (PoctOR25, PexcOR14) by qPCR. PAML analysis conducted on male-biased ORs indicated positive selection acting on the male-biased OR7. The fact that OR7 is likely under positive selection, that it is male-biased in its expression and that its orthologue in C. obliquana, CoblOR7, responds to sex pheromone components also utilised by Planotortrix species, suggests that this receptor may also be important in sex pheromone reception in Planotortrix species

Predicted transmembrane topology of OR7.

<p>Variable sites between <i>P</i>. <i>octo</i> and <i>P</i>. <i>excessana</i> are highlighted. Red dots indicate the position of amino acid substitutions in <i>P</i>. <i>octo</i>, and black dots amino acid substitutions in <i>P</i>. <i>excessana</i> compared to a predicted common ancestor. The double line indicates the transmembrane region, with extracellular and cytoplasmic sides labelled.</p

The Peripheral Olfactory Repertoire of the Lightbrown Apple Moth, Epiphyas postvittana.

The lightbrown apple moth, Epiphyas postvittana is an increasingly global pest of horticultural crops. Like other moths, E. postvittana relies on olfactory cues to locate mates and oviposition sites. To detect these cues, moths have evolved families of genes encoding elements of the peripheral olfactory reception system, including odor carriers, receptors and degrading enzymes. Here we undertake a transcriptomic approach to identify members of these families expressed in the adult antennae of E. postvittana, describing open reading frames encoding 34 odorant binding proteins, 13 chemosensory proteins, 70 odorant receptors, 19 ionotropic receptors, nine gustatory receptors, two sensory neuron membrane proteins, 27 carboxylesterases, 20 glutathione-S-transferases, 49 cytochrome p450s and 18 takeout proteins. For the odorant receptors, quantitative RT-PCR corroborated RNAseq count data on steady state transcript levels. Of the eight odorant receptors that group phylogenetically with pheromone receptors from other moths, two displayed significant male-biased expression patterns, one displayed significant female-biased expression pattern and five were expressed equally in the antennae of both sexes. In addition, we found two male-biased odorant receptors that did not group with previously described pheromone receptors. This suite of olfaction-related genes provides a substantial resource for the functional characterization of this signal transduction system and the development of odor-mediated control strategies for horticultural pests

PAML analysis of OR30 across endemic New Zealand leafroller moths.

<p>Maximum likelihood tree of OR30 othologues from <i>Ctenopseustis obliquana</i> (CoblOR30), <i>C</i>. <i>herana</i> (CherOR30), <i>Planotortrix octo</i> (PoctOR30) and <i>P</i>. <i>excessana</i> (PexcOR30). dN, dS and dN/dS values were generated using the M3 model.</p

Predicted transmembrane topology of OR30 from <i>P</i>. <i>excessana</i> and <i>P</i>. <i>octo</i>.

<p>Variable sites highlighted in red indicating amino acid substitutions in <i>P</i>. <i>octo</i>, black indicating substitutions in <i>P</i>. <i>excessana</i>, red-black indicating independent substitutions in <i>P</i>. <i>octo</i> and <i>P</i>. <i>excessana</i> compared to a predicted common ancestor. The double line indicates the transmembrane region, with extracellular and cytoplasmic sides labelled.</p

Phylogenetic analyses of odorant receptors from <i>Planotortrix octo</i>, <i>P</i>. <i>excessana Ctenopseustis obliquana</i>, <i>C</i>. <i>herana</i> and <i>Epiphyas postvittana</i>.

<p>Maximum likelihood rooted phylogeny of all odorant receptors from the five species. The tree is rooted with the odorant receptor co-receptor (Orco) The sex pheromone receptor clade is highlighted in grey, OR07 and OR30 (male biased) are highlighted in blue.</p

PAML analysis of OR7 across the endemic New Zealand leafroller moths <i>Ctenopseustis obliquana</i>, <i>C</i>. <i>herana</i>, <i>Planotortrix octo</i> and <i>P</i>. <i>excessana</i>.

<p>Maximum likelihood tree of OR7 othologues from <i>C</i>. <i>obliquana</i> (CoblOR7), <i>C</i>. <i>herana</i> (CherOR7), <i>P</i>. <i>octo</i> (PoctOR7) and <i>P</i>. <i>excessana</i> (PexcOR7). dN, dS and dN/dS values were generated using the M3 model.</p

The Genomics and Population Genomics of the Light Brown Apple Moth, Epiphyas postvittana, an Invasive Tortricid Pest of Horticulture

The light brown apple moth, Epiphyas postvittana is an invasive, polyphagous pest of horticultural systems around the world. With origins in Australia, the pest has subsequently spread to New Zealand, Hawaii, California and Europe, where it has been found on over 500 plants, including many horticultural crops. We have produced a genomic resource, to understand the biological basis of the polyphagous and invasive nature of this and other lepidopteran pests. The assembled genome sequence encompassed 598 Mb and has an N50 of 301.17 kb, with a BUSCO completion rate of 97.9%. Epiphyas postvittana has 34% of its assembled genome represented as repetitive sequences, with the majority of the known elements made up of longer DNA transposable elements (14.07 Mb) and retrotransposons (LINE 17.83 Mb). Of the 31,389 predicted genes, 28,714 (91.5%) were assigned to 11,438 orthogroups across the Lepidoptera, of which 945 were specific to E. postvittana. Twenty gene families showed significant expansions in E. postvittana, including some likely to have a role in its pest status, such as cytochrome p450s, glutathione-S-transferases and UDP-glucuronosyltransferases. Finally, using a RAD-tag approach, we investigated the population genomics of this pest, looking at its likely patterns of invasion