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•Textile industry effluents were treated in constructed wetlands (drenches) by plants.•Co-plantation of T. angustifolia and P. scrobiculatum showed enhanced dye removal.•T. ...angustifolia and P. scrobiculatum decolorized Congo Red and textile effluent.•Possible degradation pathways of Congo Red by all three systems are proposed.•Phytotoxicity assay revealed less toxic nature of dye products after treatment.
Field treatment of textile industry effluent was carried out in constructed drenches (91.4m×1.2m×0.6m; 65.8m3) planted independently with Typha angustifolia, Paspalum scrobiculatum and their co-plantation (consortium-TP). The in situ treatment of effluent by T. angustifolia, P. scrobiculatum and consortium-TP was found to decrease ADMI color value by 62, 59 and 76%, COD by 65, 63 and 70%, BOD by 68, 63 and 75%, TDS by 45, 39 and 57%, and TSS by 35, 31 and 47%, respectively within 96h. Heavy metals such as arsenic, cadmium, chromium and lead were also removed up to 28–77% after phytoremediation. T. angustifolia and P. scrobiculatum showed removal of Congo Red (100mg/L) up to 80 and 73%, respectively within 48h while consortium-TP achieved 94% decolorization. Root tissues of T. angustifolia and P. scrobiculatum revealed inductions in the activities of oxido-reductive enzymes such as lignin peroxidase (193 and 32%), veratryl alcohol oxidase (823 and 460%), laccase (492 and 182%) and azo reductase (248 and 83%), respectively during decolorization of Congo Red. Anatomical studies of roots, FTIR, HPLC, UV–vis Spectroscopy and GC–MS analysis verified the phytotransformation. Phytotoxicity studies confirmed reduced toxicity of the metabolites of Congo Red.
The genome of the major agricultural weed species, annual ryegrass (
Lolium rigidum
) was assembled, annotated and analysed. Annual ryegrass is a major weed in grain cropping, and has the remarkable ...capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44 Gb with N
50
= 361.79 Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome of
L. rigidum
is a critical asset for leveraging genetic information for the management of this highly problematic weed species.
Chromosomal inversion polymorphisms are common in animals and plants, and recent models suggest that alternative arrangements spread by capturing different combinations of alleles acting additively ...or epistatically to favour local adaptation. It is also thought that inversions typically maintain favoured combinations for a long time by suppressing recombination between alternative chromosomal arrangements. Here, we consider patterns of linkage disequilibrium and genetic divergence in an old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known to be associated with climate change adaptation and a recent invasion event into Australia. We extracted, karyotyped and sequenced whole chromosomes from two Australian populations, so that changes in the arrangement of the alleles between geographically separated tropical and temperate areas could be compared. Chromosome‐wide linkage disequilibrium (LD) analysis revealed strong LD within the region spanned by In(3R)Payne. This genomic region also showed strong differentiation between the tropical and the temperate populations, but no differentiation between different karyotypes from the same population, after controlling for chromosomal arrangement. Patterns of differentiation across the chromosome arm and in gene ontologies were enhanced by the presence of the inversion. These data support the notion that inversions are strongly selected by bringing together combinations of genes, but it is still not clear if such combinations act additively or epistatically. Our data suggest that climatic adaptation through inversions can be dynamic, reflecting changes in the relative abundance of different forms of an inversion and ongoing evolution of allelic content within an inversion.
We use the genomes of 160 insect species to test the hypothesis that the size of detoxifying enzyme families is greater in species using more chemically diverse food resources. Phylogenetically ...appropriate contrasts in subsamples of the data generally support the hypothesis. We find relatively high numbers of cytochrome P450, glutathione S-transferase and carboxyl/choline esterase genes in omnivores and herbivores feeding on chemically complex tissues and relatively low numbers of these genes in specialists on relatively simple diets, including plant sap, nectar and pollen, and blood. Among Lepidoptera feeding on green plant tissue and Condylognatha feeding on sap we also find more of these genes in highly polyphagous species, many of which are major agricultural pests. These genomic signatures of food resource use are consistent with the hypothesis that some taxa are preadapted for insecticide resistance evolution.
Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by its chronological detection across the Old World and the hypothesis of ...an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range. 870 high-quality nuclear single nucleotide polymorphic DNA markers identified five distinct New World population clusters, broadly reflecting FAW native geographical ranges and the absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinning the pest's global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated the potential of population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar ...evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species
and
. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.
Fimbristylis dichotoma, Ammannia baccifera and their co-plantation consortium FA independently degraded Methyl Orange, simulated dye mixture and real textile effluent. Wild plants of F. dichotoma and ...A. baccifera with equal biomass showed 91% and 89% decolorization of Methyl Orange within 60h at a concentration of 50ppm, while 95% dye removal was achieved by consortium FA within 48h. Floating phyto-beds with co-plantation (F. dichotoma and A. baccifera) for the treatment of real textile effluent in a constructed wetland was observed to be more efficient and achieved 79%, 72%, 77%, 66% and 56% reductions in ADMI color value, COD, BOD, TDS and TSS of textile effluent, respectively. HPTLC, GC-MS, FTIR, UV–vis spectroscopy and activated oxido-reductive enzyme activities confirmed the phytotrasformation of parent dye in to new metabolites. T-RFLP analysis of rhizospheric bacteria of F. dichotoma, A. baccifera and consortium FA revealed the presence of 88, 98 and 223 genera which could have been involved in dye removal. Toxicity evaluation of products formed after phytotransformation of Methyl Orange by consortium FA on bivalves Lamellidens marginalis revealed less damage of the gills architecture when analyzed histologically. Toxicity measurement by Random Amplification of Polymorphic DNA (RAPD) technique revealed bivalve DNA banding pattern in treated Methyl Orange sample suggesting less toxic nature of phytotransformed dye products.
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•F. dichotoma L. and A. baccifera L. decolorized Methyl Orange and real textile dye effluent.•Co-plantation of F. dichotoma L. and A. baccifera L. gave more efficient dye removal.•Possible degradation pathways of Methyl Orange by all three systems are proposed.•Effluents were treated note-worthily in floating phyto-beds by plants.•Toxicity study on bivalve revealed less toxic nature of dye products.
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high‐quality ...assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome‐wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert‐adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate‐continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics‐restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large‐scale and multifaceted genomic changes.
Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to ...resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue prediction remains an ongoing challenge.
Here we present Orthonome, an orthologue prediction pipeline, designed to reduce the trade-off between orthologue capture rates (recall) and accuracy of multi-species orthologue prediction. The pipeline compares sequence domains and then forms sequence-similar clusters before using phylogenetic comparisons to identify inparalogues. It then corrects sequence similarity metrics for fragment and gene length bias using a novel scoring metric capturing relationships between full length as well as fragmented genes. The remaining genes are then brought together for the identification of orthologues within a phylogenetic framework. The orthologue predictions are further calibrated along with inparalogues and gene births, using synteny, to identify novel orthologous relationships. We use 12 high quality Drosophila genomes to show that, compared to other orthologue prediction pipelines, Orthonome provides orthogroups with minimal error but high recall. Furthermore, Orthonome is resilient to suboptimal assembly/annotation quality, with the inclusion of draft genomes from eight additional Drosophila species still providing >6500 1:1 orthologues across all twenty species while retaining a better combination of accuracy and recall than other pipelines. Orthonome is implemented as a searchable database and query tool along with multiple-sequence alignment browsers for all sets of orthologues. The underlying documentation and database are accessible at http://www.orthonome.com .
We demonstrate that Orthonome provides a superior combination of orthologue capture rates and accuracy on complete and draft drosophilid genomes when tested alongside previously published pipelines. The study also highlights a greater degree of evolutionary conservation across drosophilid species than earlier thought.
Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with ...such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species.
We find disproportionately high rates of gene gains in internal branches in the species' phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species' differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one.
Adaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.
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