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BackgroundHalyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

BackgroundThe Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.ResultsWe use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.ConclusionThe AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Objective: The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America. Although partial transcriptome data are available for this pest, a genome assembly was not available for this species. This assembly of a high-quality chromosome-length genome of TPB is aimed to develop the genetic resources that can provide the foundation required for advancing research on this species. Results: The initial genome of TPB assembled with paired-end nucleotide sequences generated with Illumina technology was scaffolded with Illumina HiseqX reads generated from a proximity ligated (HiC) library to obtain a high-quality genome assembly. The final assembly contained 3963 scaffolds longer than 1 kbp to yield a genome of 599.96 Mbp. The N50 of the TPB genome assembly was 35.64 Mbp and 98.68% of the genome was assembled into 17 scaffolds larger than 1 Mbp. This megabase scaffold number is the same as the number of chromosomes observed in karyotyping of this insect. The TPB genome is known to have high repetitive DNA content, and the reduced assembled genome size compared to flowcytometric estimates of approximately 860 Mbp may be due to the collapsed assembly of highly similar regions. [ABSTRACT FROM AUTHOR]

Dramatic genome size variation exists across the Tree of Life. Some crustacean groups, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that genome sizes may be constrained due to physiological pressures. This may indicate that a general "genome-temperature-size" rule exists in ectotherms, in which body-size and latitude may be predictive of genome size. We examined the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncovered a 6-fold genome size variation within Haustoriidae, a substantial amount considering this clade is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. We also found evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays. [ABSTRACT FROM AUTHOR]

The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalizations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed these data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes, and that orders exhibit striking differences in rates of fusions, fissions and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups. [ABSTRACT FROM AUTHOR]

Background: Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe. Results: By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~ 38% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433–551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in C. felis. Similarly, broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads, we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas. Conclusion: Rampant CNV in C. felis has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel Wolbachia endosymbionts—potential tools for blocking pathogen transmission—these oddities highlight a unique and underappreciated disease vector. [ABSTRACT FROM AUTHOR]

Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elementswere evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies. [ABSTRACT FROM AUTHOR]

Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships. [ABSTRACT FROM AUTHOR]

We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions. [ABSTRACT FROM AUTHOR]

Flow cytometry was used to study the genome sizes and ploidy levels for four thrips species: Franklinothrips orizabensis Johansen ( Thysanoptera: Aeolothripidae), Frankliniella occidentalis Pergande, Frankliniella fusca Hinds, and Thrips tabaci Lindeman ( Thysanoptera: Thripidae). F. orizabensis males and females had 1 C genome sizes of 426 Mb and 422 Mb, respectively. Male and female F. fusca had 1 C genome sizes of 392 Mb and 409 Mb, whereas F. occidentalis males and females had smaller 1 C genomes that were 345 Mb and 337 Mb, respectively. Male F. orizabensis, F. occidentalis and F. fusca were haploid and females diploid. Five isofemale lines of T. tabaci, initiated from parthenogenetic, thelytokous females and collected from different locations in North Carolina, were included in this study; no males were available. One isofemale line was diploid with a genome size of 1 C = 310 Mb, and the other four had a mean genome size of 1 C = 482 Mb, which is consistent with evidence from microsatellite data of diploidy and polyploidy, respectively, in these same five thelytokous lines. This is the first study to produce genome size estimates for thysanopteran species, and report polyploidy in T. tabaci populations. [ABSTRACT FROM AUTHOR]

Drosophila melanogaster Meigen, 1830 has served as a model insect for over a century. Sequencing of the 11 additional Drosophila Fallen, 1823 species marks substantial progress in comparative genomics of this genus. By comparison, practically nothing is known about the genome size or genome sequences of parasitic wasps of Drosophila. Here, we present the first comparative analysis of genome size and karyotype structures of Drosophila parasitoids of the Leptopilina Förster, 1869 and Ganaspis Förster, 1869 species. The gametic genome size of Ganaspis xanthopoda (Ashmead, 1896) is larger than those of the three Leptopilina species studied. The genome sizes of all parasitic wasps studied here are also larger than those known for all Drosophila species. Surprisingly, genome sizes of these Drosophila parasitoids exceed the average value known for all previously studied Hymenoptera. The haploid chromosome number of both Leptopilina heterotoma (Thomson, 1862) and L. victoriae Nordlander, 1980 is ten. A chromosomal fusion appears to have produced a distinct karyotype for L. boulardi (Barbotin, Carton et Keiner-Pillault, 1979) (n = 9), whose genome size is smaller than that of wasps of the L. heterotoma clade. Like L. boulardi, the haploid chromosome number for G. xanthopoda is also nine. Our studies reveal a positive, but non linear, correlation between the genome size and total chromosome length in Drosophila parasitoids. These Drosophila parasitoids differ widely in their host range, and utilize different infection strategies to overcome host defense. Their comparative genomics, in relation to their exceptionally well-characterized hosts, will prove to be valuable for understanding the molecular basis of the host-parasite arms race and how such mechanisms shape the genetic structures of insect communities. [ABSTRACT FROM AUTHOR]

We report the genome size and the GC content, and perform a phylogenetic analysis on Botryococcus braunii Kütz., a green, colony-forming, hydrocarbon-rich alga that is an attractive source for biopetroleum. While the chemistry of the hydrocarbons produced by the B race of B. braunii has been studied for many years, there is a deficiency of information concerning the molecular biology of this alga. In addition, there has been some discrepancy as to the phylogenetic placement of the Berkeley (or Showa) strain of the B race. To clarify its classification, we isolated the Berkeley strain nuclear SSU (18S) rRNA gene and β-actin cDNA and used these sequences for phylogenetic analysis to determine that the Berkeley strain belongs to the Trebouxiophyceae class. This finding is in agreement with other B races of B. braunii, indicating the Berkeley strain is a true B race of B. braunii. To better understand molecular aspects of B. braunii, we obtained the Berkeley strain genome size as a first step in genome sequencing. Using flow cytometry, we determined the B. braunii Berkeley genome size to be 166.2 ± 2.2 Mb. We also estimated the GC content of the Berkeley strain as 54.4 ± 1.2% for expressed gene sequences. [ABSTRACT FROM AUTHOR]

Abstract: The suborder Ixodida includes many tick species of medical and veterinary importance, but little is known about the genomic characteristics of these ticks. We report the first study to determine genome size in two species of Argasidae (soft ticks) and seven species of Ixodidae (hard ticks) using flow cytometry analysis of fluorescent stained nuclei. Our results indicate a large haploid genome size (1C>1000Mbp) for all Ixodida with a mean of 1281Mbp (1.31±0.07pg) for the Argasidae and 2671Mbp (2.73±0.04pg) for the Ixodidae. The haploid genome size of Ixodes scapularis was determined to be 2262Mbp. We observed inter- and intra-familial variation in genome size as well as variation between strains of the same species. We explore the implications of these results for tick genome evolution and tick genomics research. [Copyright &y& Elsevier]

Using flow cytometry, the genome sizes of two species of Strepsiptera were studied: that of maleCaenocholax fenyesi texensisKathirithamby&Johnston (Myrmecolacidae) at 108 Mb, which is the smallest insect genome documented to date; and those of male and femaleXenos vesparumRossi (Stylopidae), which are 1C = 130 and 133 Mb, respectively. The genome sizes of the following were analysed for comparative purposes: (a) the Hessian fly,Mayetiola destructor(Say), which was previously reported to be the smallest among insects: the male measured at 1C = 121 Mb and the female at 1C = 158 Mb; and (b) the female parasitic, haplodiploid, microhymenopteran wasp,Trichogramma brassicaeBezdenko, which measured at 1C = 246 Mb. The hosts of the strepsipterans were also measured: maleSolenopsis invictaBuren, the red imported fire ant (host of maleC. f. texensis), which is 1C = 753.3 Mb, and femalePolistes dominulusChrist, the paper wasp (host ofX. vesparum), is 1C = 301.4 Mb. Endoreduplication (4C) of the genome of the thorax of the male strepsipteran, and higher levels of endoduplication (4, 8, 16C) in the body of the larger female was observed. In contrast, little or no endoreduplication was observed, either in the Hessian fly, or in the parasitic wasp. [ABSTRACT FROM AUTHOR]

Drosophila underreplicate the DNA of thoracic nuclei, stalling during S phase at a point that is proportional to the total genome size in each species. In polytene tissues, such as the Drosophila salivary glands, all of the nuclei initiate multiple rounds of DNA synthesis and underreplicate. Yet, only half of the nuclei isolated from the thorax stall; the other half do not initiate S phase. Our question was, why half? To address this question, we use flow cytometry to compare underreplication phenotypes between thoracic tissues. When individual thoracic tissues are dissected and the proportion of stalled DNA synthesis is scored in each tissue type, we find that underreplication occurs in the indirect flight muscle, with the majority of underreplicated nuclei in the dorsal longitudinal muscles (DLM). Half of the DNA in the DLM nuclei stall at S phase between the unreplicated G0 and fully replicated G1. The dorsal ventral flight muscle provides the other source of underreplication, and yet, there, the replication stall point is earlier (less DNA replicated), and the endocycle is initiated. The differences in underreplication and ploidy in the indirect flight muscles provide a new tool to study heterochromatin, underreplication and endocycle control. [ABSTRACT FROM AUTHOR]

Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions. [ABSTRACT FROM AUTHOR]

The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the 'C-value paradox'. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4-5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution. [ABSTRACT FROM AUTHOR]

Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry. [ABSTRACT FROM AUTHOR]

Genome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a consequence, the relationship between genome size and differences in chromosome number or inter-sexual differences attributed to XY systems are largely unstudied. We hypothesize that structural differences associated with chromosome number and X-Y chromosome differentiation, should result in differing rates and patterns of genome size change. In this study, we utilize the subgenera within the Drosophila to ask if patterns and rates of genome size change differ between closely related species with differences in chromosome numbers and states of the XY system. Genome sizes for males and females of 152 species are used to answer these questions (with 92 newly added or updated estimates). While we find no relationship between chromosome number and genome size or chromosome number and inter-sexual differences in genome size, we find evidence for differing patterns of genome size change between the subgenera, and increasing rates of change throughout time. Estimated shifts in rates of change in sex differences in genome size occur more often in Sophophora and correspond to known neo-sex events. [ABSTRACT FROM AUTHOR]

The cowpea bruchid ( Callosobruchus maculatus ) is the most important storage pest of grain legumes and comprises geographically distinct strains. Storage under a modified atmosphere with decreased O 2 content represents an alternative to chemical fumigants for pest control of stored grains. In this study, we compared reproduction, development and survival, as well as genome size of bruchid strains from South India (SI), Burkina Faso (BF), Niger (CmNnC) and the United States (OH), reared on mung bean ( Vigna radiata ). Fecundity and egg-to-adult duration varied significantly among these strains. Notably, strain BF had the highest fecundity, and strain SI displayed the fastest development whereas strain OH was the slowest. Differences in adult lifespan among strains were only detected in unmated but not in the mated group. Genome size of SI females was significantly larger than that of OH females, and for all four strains, the female genomes were larger than those of their corresponding males. Furthermore, we studied effects of exposure to 1% O 2 + 99% N 2 on strains SI and BF. Mortality caused by hypoxia was influenced by not only developmental stage but also by insect strain. Eggs were most sensitive, particularly at the early stage, whereas the 3rd and 4th instar larvae were most tolerant and could survive up to 15 days of low O 2 . Strain SI was slightly more resistant than BF in egg and larval stages. Proteolytic activity prior to, during and after hypoxia treatment revealed remarkable metabolic plasticity of cowpea bruchids in response to modified atmosphere. [ABSTRACT FROM AUTHOR]