N 6-methyladenosine (m 6A) is a common messenger RNA (mRNA) modification that affects diverse physiological processes in stress responses. However, the role of m 6A modification in plants coping with herbivore stress remains unclear. Here we found that an infestation of brown planthopper (BPH) Nilaparvata lugens female adults enhanced the rice resistance to BPH. An m 6A methylome analysis of BPH-infested and un-infested rice samples were measured to explore the interaction between rice and BPH. m 6A methylation occurs mainly in genes actively expressed in rice following BPH infestation, while an analysis of the whole-genomic mRNA distribution of m 6A showed that BPH infestation caused an overall decrease in the number of m 6A methylation sites across the chromosomes. Genes involved in components of the m 6A modification machinery, BPH resistance, and several defense-related (such as JA, SA and cellulose) pathways were heavily methylated by m 6A in BPH-infested rice compared to those in un-infested rice. In contrast, m 6A modification levels of growth-related phytohormones (auxin and gibberellin) biosynthesis-related genes were significantly attenuated under BPH attack, accompanied by downregulated expression of these transcripts, indicating that rice growth was restricted during BPH attack to rapidly optimize resource allocation for plant defense. Integrative analysis of the differential patterns of m 6A methylation and the corresponding transcripts showed a positive correlation between m 6A methylation and transcriptional regulation. In conclusion, the process of m 6A modification acts as an important strategy for regulating expression of genes involved in rice defense and growth during rice-BPH interaction.

Low vagility species may hold strong genetic signatures of past biogeographic processes but are also vulnerable to habitat loss. Flightless grasshoppers of the morabine group were once widespread in south-eastern Australia including Tasmania but are becoming restricted to remnant patches of vegetation, with local ranges impacted by agriculture and development as well as management. Habitat fragmentation can generate genetically differentiated “island” populations with low genetic variation. However, following revegetation, populations could be re-established and gene flow increased. Here we characterise SNP based genetic variation in a widespread chromosomal race of the morabine Vandiemenella viatica (race 19) to investigate the genetic health of remnant populations and to provide guidelines for restoration efforts. We update the distribution of this race to new sites in Victoria and Tasmania, and show that V. viatica populations from northern Tasmania and eastern Victoria have reduced genetic variation compared to other mainland populations. In contrast there was no effect of habitat fragment size on genetic variation. Tasmanian V. viatica populations fell into two groups, one connected genetically to eastern Victoria and the other connected to south-western Victoria. Mainland populations showed isolation by distance. These patterns are consistent with expectations from past biogeographic processes rather than local recent population fragmentation and emphasize the importance of small local reserves in preserving genetic variation. The study highlights how genomic analyses can combine information on genetic variability and population structure to identify biogeographic patterns within a species, which in turn can inform decisions on potential source populations for translocations.

Infectious diseases are recognised as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (Haliotis rubra) following a major population crash associated with an infectious disease. A genome wide association study on H. rubra was conducted using pooled whole genome re-sequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus-1 (HaHV-1). Approximately 25,000 SNP loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV-1 immunity in the New Zealand pāua (H. iris) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in H. rubra fishing stocks decimated by HaHV-1, with stock recovery determined by rapid evolutionary changes leading to virus resistance. This is a novel example of rapid adaptation in natural populations of a non-model marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities.

Conservation research is dominated by vertebrate examples but the shorter generation times and high local population sizes of invertebrates may lead to different management strategies. Here we investigate the genetic structure of an endangered flightless grasshopper, Keyacris scurra, used in classical evolutionary studies in the 60s. It had a wide distribution across New South Wales (NSW) and Victoria in pre-European times but has now become threatened because of land clearing for agriculture. We revisited remnant sites of K. scurra, with populations now restricted to only one area in Victoria and a few small patches in NSW and the Australian Capital Territory (ACT). Using DArTseq to generate SNP markers as well as mtDNA sequence data, we show that the remaining Victorian populations in an isolated valley are genetically distinct from the NSW populations and that all populations are genetically unique, with large FST values up to 0.8. We also find that, with one exception, the NSW/ACT populations separate genetically into chromosomal races (2n = 15 vs. 2n = 17). Isolation by distance was detected across both the SNP and mtDNA data sets, and there was substantial differentiation within chromosomal races. Genetic diversity as measured by heterozygosity was not correlated with the size of remaining habitat patches, with high variation present in some remnant cemetery sites. However, inbreeding correlated negatively with estimated habitat size at 25-500 m patch radius. These findings emphasize the importance of small fragments in conserving genetic variation across the species, and they highlight populations suitable for future translocations.

Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and A. loripes were settled and exposed to ambient or elevated temperature and pCO2 conditions for seven months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on samples from the same experiment and showed that gene expression of the hybrid Acropora also showed clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO2 conditions.

The peach fruit moth (PFM), Carposina sasakii Matsumura, is a major phytophagous orchard pest widely distributed across Northeast Asia. Here, we report the chromosome-level genome for the PFM, representing the first genome for the family Carposinidae, from the lepidopteran superfamily Copromorphoidea. The genome was assembled into 404.83 Mb sequences using PacBio long-read and Illumina short-read sequences, including 275 contigs, with a contig N50 length of 2.62 Mb. All contigs were assembled into 32 linkage groups assisted by the Hi-C technique, including 30 autosomes, a female-specific W chromosome and a Z chromosome. BUSCO analysis showed that 98.2% genes were complete and 0.4% of genes were fragmented, while 1.4% of genes were missing in the assembled genome. In total, 23,218 protein-coding genes were predicted, of which 82.72% were functionally annotated. Because of the importance of diapause triggered by photoperiod in PFM, five circadian genes in the PFM as well as in the other related species were annotated, and potential genes related to diapause and photoperiodic reaction were also identified from transcriptome sequencing. In addition, manual annotation of detoxification gene families was undertaken and showed a higher number of ABC and GST genes in PFM than in most other lepidopterans, in contrast to a lower number of UGT genes, suggesting different detoxication pathways in this moth. The high-quality genome provides a resource for comparative evolutionary studies of this moth and its relatives within the context of radiations across Lepidoptera.

Macroinvertebrate biodiversity is routinely used to assess the ecological condition of freshwater environments. Macroinvertebrates are traditionally identified morphologically to mostly family level but using DNA metabarcoding they can be rapidly and reliably identified to species. Developing standardised, robust and cost-effective protocols would enable DNA metabarcoding to be broadly used for routine freshwater biological assessments leading to both potential cost savings as well as increased taxonomic resolution. To further reduce the cost and time it takes to process samples, we examine the feasibility of DNA metabarcoding unsorted macroinvertebrates (macroinvertebrates and debris) from sweep net samples collected from stream pool or edge habitats. We processed these unsorted samples with a standardised method and tested multiple primer sets widely used for invertebrate DNA metabarcoding. We found that currently available DNA metabarcoding primers are well suited for processing unsorted samples, though some performed better than others. However, macroinvertebrate density affected the number of species detected with DNA metabarcoding, particularly the detection of rare taxa. These findings show that DNA metabarcoding of unsorted net contents could streamline macroinvertebrate sample processing for bioassessment, but the optimal amounts of unsorted material for sub-sampling needs to be considered when assessing macroinvertebrate biodiversity.

Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and A. loripes were settled and exposed to ambient or elevated temperature and pCO2 conditions for seven months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on samples from the same experiment and showed that gene expression of the hybrid Acropora also showed clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO2 conditions.