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The breadwinner : a graphic novel
Young Parvana lives with her family in one room of a bombed-out apartment building in Kabul, Afghanistan. Because Parvana's father has a foreign education, he is arrested by the Taliban. Women cannot appear in public unless covered head to toe, go to school, or work outside the home, so the family becomes increasingly desperate until Parvana conceives a plan.
Book
Preservation Time on Ice Impacts Global Gene Expression in Oyster Spat
The pearling industry is one of Australia's most valuable and iconic industries, creating significant economic and employment opportunities across Northern Australia. To improve our understanding of the relationship between the silver‐lipped pearl oyster and its biotic and abiotic environment using transcriptomics, oyster spat are collected weekly from several offshore sites in Northwestern Australia. However, due to the remoteness of the farming locations, collected spat must be transported on ice for intervals before snap‐freezing becomes possible. In this study, we investigate the impact of incubation on ice for intervals of up to 90 min on the global gene expression of collected spat. Preserving spat on ice for up to 90 min did not significantly impact the RNA concentration or quality. On average, more than 100 ng/µL of RNA (RIN 7.0–8.5) was extracted per sample to generate sequencing libraries, and no significant impact on sequencing and mapping reads to the genome was observed between treatments. However, prolonged incubation on ice did alter gene expression, with a significant increase in differential gene expression observed after 60 min. Furthermore, changes in the number of predicted genes, potentially in response to stress and cold, including stress‐related heat shock protein (HSP) and Cytochrome P450 (CYP) genes, immune‐related perlucin‐like genes, and solute carrier (SLC) transporters, were observed with prolonged incubation. The observed stress‐induced changes can alter the global gene expression status of the spat at the time of collection and may lead to misinterpretations upon analysing the impact of abiotic and biotic factors on the health of silver‐lipped pearl oyster spat. Prolonged incubation intervals of oyster spat on ice destined for RNASeq analysis are therefore not recommended. Remote sites for longitudinal and comparative studies were therefore selected with this guideline in mind. This study also demonstrates the importance of conducting pilot trials in the development of research study protocols.
Journal Article
Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African–Australian biotic exchange
Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic diversity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic diversity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced samples to be most closely related to the southern‐most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an unsampled ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic diversity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes. Bitou bush is a coastal shrub, native to Southern Africa, and invasive in Australia. We used single nucleotide polymorphisms to reconstruct the invasion history of bitou bush into eastern and Western Australia. We found strong genetic structure in the native range, and detected bottlenecks through the introduction process. Our results highlight the risk of introduction of potentially invasive species via shipping routes, even from a small number of propagules.
Journal Article
Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus
Background
Brassica napus
is an important oilseed crop cultivated worldwide. During domestication and breeding of
B. napus
, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in
B. napus
. An F
2
mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.
Results
Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including
FLC
.
Conclusions
These findings demonstrate the effectiveness of the ddRAD approach to sample the
B. napus
genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F
2
populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
Journal Article
Insights into the transcriptomic responses of silver-lipped pearl oysters Pinctada maxima exposed to a simulated large-scale seismic survey
Background
The wild stocks of
Pinctada maxima
pearl oysters found off the coast of northern Australia are of critical importance for the sustainability of Australia’s pearling industry. Locations inhabited by pearl oysters often have oil and gas reserves in the seafloor below and are therefore potentially subjected to seismic exploration surveys. The present study assessed the impact of a simulated commercial seismic survey on the transcriptome of pearl oysters. Animals were placed at seven distances (-1000, 0, 300, 500, 1000, 2000, and 6000 m) from the first of six operational seismic source sail lines. Vessel control groups were collected before the seismic survey started and exposed groups were collected after completion of six operational seismic sail lines (operated at varying distances over a four-day period). Samples from these groups were taken immediately and at 1, 3, and 6 months post-exposure. RNA-seq was used to identify candidate genes and pathways impacted by the seismic noise in pearl oyster mantle tissues. The quantified transcripts were compared using DESeq2 and pathway enrichment analysis was conducted using KEGG pathway, identifying differentially expressed genes and pathways associated with the seismic activity.
Results
The study revealed the highest gene expression and pathway dysregulation after four days of exposure and a month post-exposure. However, this dysregulation diminished after three months, with only oysters at -1000 and 0 m displaying differential gene expression and pathway disruption six months post-exposure. Stress-induced responses were evident and impacted energy production, transcription, translation, and protein synthesis.
Conclusion
Seismic activity impacted the gene expression and pathways of pearl oysters at distances up to 2000 m from the source after four days of exposure, and at distances up to 1000 m from the source one-month post-exposure. At three- and six-months post-exposure, gene and pathway dysregulations were mostly observed in oysters located closest to the seismic source at 0 and − 1000 m. Overall, our results suggest that oysters successfully activated stress responses to mitigate damage and maintain cellular homeostasis and growth in response to seismic noise exposure.
Journal Article
Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS‐Lep2
Brassica napus (oilseed rape, canola) seedling resistance to Leptosphaeria maculans, the causal agent of blackleg (stem canker) disease, follows a gene‐for‐gene relationship. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the resistance genes RlmS and LepR2, respectively, present in B. napus ‘Surpass 400’. Here we report cloning of AvrLmS and AvrLep2 using two independent methods. AvrLmS was cloned using combined in vitro crossing between avirulent and virulent isolates with sequencing of DNA bulks from avirulent or virulent progeny (bulked segregant sequencing). AvrLep2 was cloned using a biparental cross of avirulent and virulent L. maculans isolates and a classical map‐based cloning approach. Taking these two approaches independently, we found that AvrLmS and AvrLep2 are the same gene. Complementation of virulent isolates with this gene confirmed its role in inducing resistance on Surpass 400, Topas‐LepR2, and an RlmS‐line. The gene, renamed AvrLmS‐Lep2, encodes a small cysteine‐rich protein of unknown function with an N‐terminal secretory signal peptide, which is a common feature of the majority of effectors from extracellular fungal plant pathogens. The AvrLmS‐Lep2/LepR2 interaction phenotype was found to vary from a typical hypersensitive response through intermediate resistance sometimes towards susceptibility, depending on the inoculation conditions. AvrLmS‐Lep2 was nevertheless sufficient to significantly slow the systemic growth of the pathogen and reduce the stem lesion size on plant genotypes with LepR2, indicating the potential efficiency of this resistance to control the disease in the field. AvrLmS‐Lep2, the 10th cloned Leptosphaeria maculans AVR gene, was easily identified by bulk sequencing, and induces a fluctuating phenotype on rapeseed cotyledons that nevertheless limits stem canker severity.
Journal Article
Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution
In adapting to a marine environment, two independent seagrass lineages lost genes associated with ethylene and terpenoid biosynthesis and retained genes related to salinity adaptation, suggesting habitat-driven convergent evolution.
Abstract
Seagrasses are marine angiosperms that live fully submerged in the sea. They evolved from land plant ancestors, with multiple species representing at least three independent return-to-the-sea events. This raises the question of whether these marine angiosperms followed the same adaptation pathway to allow them to live and reproduce under the hostile marine conditions. To compare the basis of marine adaptation between seagrass lineages, we generated genomic data for Halophila ovalis and compared this with recently published genomes for two members of Zosteraceae, as well as genomes of five non-marine plant species (Arabidopsis, Oryza sativa, Phoenix dactylifera, Musa acuminata, and Spirodela polyrhiza). Halophila and Zosteraceae represent two independent seagrass lineages separated by around 30 million years. Genes that were lost or conserved in both lineages were identified. All three species lost genes associated with ethylene and terpenoid biosynthesis, and retained genes related to salinity adaptation, such as those for osmoregulation. In contrast, the loss of the NADH dehydrogenase-like complex is unique to H. ovalis. Through comparison of two independent return-to-the-sea events, this study further describes marine adaptation characteristics common to seagrass families, identifies species-specific gene loss, and provides molecular evidence for convergent evolution in seagrass lineages.
Journal Article
Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)
Background and aims
Hakea prostrata
(Proteaceae) is a highly phosphorus-use-efficient plant native to southwest Australia. It maintains a high photosynthetic rate at low leaf phosphorus (P) and exhibits delayed leaf greening, a convergent adaptation that increases nutrient-use efficiency. This study aimed to provide broad physiological and gene expression profiles across leaf development, uncovering pathways leading from young leaves as nutrient sinks to mature leaves as low-nutrient, energy-transducing sources.
Methods
To explore gene expression underlying delayed greening, we analysed a de novo transcriptome for
H. prostrata
across five stages of leaf development. Photosynthesis and respiration rates, and foliar pigment, P and nitrogen (N) concentrations were determined, including the division of P into five biochemical fractions.
Key results
Transcripts encoding functions associated with leaf structure generally decreased in abundance across leaf development, concomitant with decreases in foliar concentrations of 85% for anthocyanins, 90% for P and 70% for N. The expression of genes associated with photosynthetic function increased during or after leaf expansion, in parallel with increases in photosynthetic pigments and activity, much later in leaf development than in species that do not have delayed greening. As leaves developed, transcript abundance for cytosolic and mitochondrial ribosomal proteins generally declined, whilst transcripts for chloroplast ribosomal proteins increased.
Conclusions
There was a much longer temporal separation of leaf cell growth from chloroplast development in
H. prostrata
than is found in species that lack delayed greening. Transcriptome-guided analysis of leaf development in
H. prostrata
provided insight into delayed greening as a nutrient-saving strategy in severely phosphorus-impoverished landscapes.
Journal Article
Combining multiple lines of evidence to elucidate the origin and introduction pathway of bitou bush (Chrysanthemoides monilifera subsp. rotundata) in Australia
Understanding the historical context of biological invasions can improve weed management outcomes. In this study, we aim to identify the introduction pathway of bitou bush (Chrysanthemoides monilifera subsp. rotundata) into Australia and its biogeographical origin in southern Africa by combining multiple lines of evidence from genomic tools and historical documentation. Geographic structure of genomic diversity based on SNPs supported the previous analysis of the invasion pathway of bitou bush between the two countries and within Australia, namely that all Australian material originated from the southern part of the South African distribution. Our synthesis of historical records points to the introduction of this plant into eastern Australia in Newcastle, New South Wales, from its native range in South Africa, via dry shipping ballast in about 1900. Variation in the chloroplast genome was also informative as to the biogeographical origin of Australian material and the context of the introduction. Ten unique haplotypes were discovered in South Africa with only one occurring throughout Australia, indicating an introduction from a single source population to eastern Australia. The matching haplotype was from East London, a port in South Africa with documented shipping connections to Newcastle in eastern Australia, where the weed was first recorded. Historical records suggest that the most plausible explanation for the origins of the isolated bitou bush population in Western Australia is via the shipping of steel billets or landscape plantings associated with shipping companies. The most likely introduction pathway linked the eastern Australian steel processing ports of Newcastle or Port Kembla to the Western Australian port of Kwinana in 1995. Discovering the origin and pathway of bitou bush invasions in Australia opens new opportunities for sourcing biological control agents with a higher chance of impact as well as identifying additional quarantine measures to improve outcomes and reduce long-term costs to management.
Journal Article
The pangenome of an agronomically important crop plant Brassica oleracea
There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the
Brassica oleracea
pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.
Brassica oleracea
is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing
B. oleracea
reference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits
Journal Article