Differential transcriptomic responses to heat stress in surface and subterranean diving beetles

Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CTmax 38°C cf. 42–46°C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35°C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales

Eradication of chronic myeloid leukemia stem cells: a novel mathematical model predicts no therapeutic benefit of adding G-CSF to imatinib

Imatinib mesylate induces complete cytogenetic responses in patients with chronic myeloid leukemia (CML), yet many patients have detectable BCR-ABL transcripts in peripheral blood even after prolonged therapy. Bone marrow studies have shown that this residual disease resides within the stem cell compartment. Quiescence of leukemic stem cells has been suggested as a mechanism conferring insensitivity to imatinib, and exposure to the Granulocyte-Colony Stimulating Factor (G-CSF), together with imatinib, has led to a significant reduction in leukemic stem cells in vitro. In this paper, we design a novel mathematical model of stem cell quiescence to investigate the treatment response to imatinib and G-CSF. We find that the addition of G-CSF to an imatinib treatment protocol leads to observable effects only if the majority of leukemic stem cells are quiescent; otherwise it does not modulate the leukemic cell burden. The latter scenario is in agreement with clinical findings in a pilot study administering imatinib continuously or intermittently, with or without G-CSF (GIMI trial). Furthermore, our model predicts that the addition of G-CSF leads to a higher risk of resistance since it increases the production of cycling leukemic stem cells. Although the pilot study did not include enough patients to draw any conclusion with statistical significance, there were more cases of progression in the experimental arms as compared to continuous imatinib. Our results suggest that the additional use of G-CSF may be detrimental to patients in the clinic

The evolution of epigean and stygobitic species of Koonunga Sayce, 1907 (Syncarida: Anaspidacea) in Southern Australia, with the description of three new species

Three new species of Koonunga were discovered in surface and subterranean waters in southern Australia, and were defined using mtDNA analyses and morphology. The new species are: Koonunga hornei Leijs & King; K. tatiaraensis Leijs & King and K. allambiensis Leijs & King. Molecular clock analyses indicate that the divergence times of the species are older than the landscape that they currently inhabit. Different scenarios explaining this apparent discrepancy are discussed in the context of the palaeography of the area. A freshwater epigean origin for Koonunga is considered the most likely hypothesis, whereby some lineages made the transition to the subterranean environment within the last few million years influenced by significant climatic cooling/drying. We discuss the possibility that one stygobitic lineage secondarily regained some of its body pigmentation as adaptation to increased photic conditions after cave collapse and forming of cenotes during the last glacial maximum.Remko Leijs, Tessa Bradford, James G. Mitchell, William F. Humphreys, Steven J. B. Cooper, Peter Goonan, Rachael A. Kin

E351-E450 raw illumina files

Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E351-E450. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper: Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143

Data from: Intragenomic ITS2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis

A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intragenomic distances between ITS2 variants, often larger than the average interspecific variation, caused difficulties in using ITS2 for species delimitation in both threshold and tree‐based approaches, and the gene was not included in the reported results of the previous DNA barcoding study. We here report on the intragenomic, and the intra‐ and interspecies, variation in ITS2 in the microgastrine genus Diolcogaster to further investigate the value of ITS2 as a marker for species delimitation and phylogenetics of the Microgastrinae. Distinctive intragenomic variant patterns were found in different species of Diolcogaster, with some species possessing a single major variant, and others possessing many divergent variants. Characterising intragenomic variation of ITS2 is critical as it is a widely used marker in hymenopteran phylogenetics and species delimitation, and large intragenomic distances such as those found in this study may obscure phylogenetic signal

E251-E300 raw illumina files

Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E251-E300. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper: Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143

Raw illumina files for E1-E50

Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E1-E50. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper: Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143

E51-E100 raw illumina files

Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E51-E100. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper: Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143

E551-E650 raw illumina files

Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E551-E650. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper: Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143