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opencc-by-4.0Dec 2021View details →

Highly Efficient Agrobacterium rhizogenes-mediated Genetic Transformation Technology Bypassing Tissue Culture in Citrus

Highly efficient genetic transformation technology is of great significance for the gene function analysis and precision breeding of crops. However, the most commonly used genetic transformation technology mediated by Agrobacterium tumefaciens in plants especially xylophyta is time-consuming and inefficient, which seriously hinders the progress of gene function analysis. In this study, a simple and highly efficient genetic transformation technology mediated by Agrobacterium rhizogenes bypassing tissue culture is described. Only 2~8 weeks were required for the whole workflow, with an average successful transformation ratio of 57% in shoots from adult plants. By using this technology, we successfully transferred plasmids containing gRNA, Cas9, and other exogenous genes into citrus, and achieved genome editing on target loci and overexpressed multiple foreign genes at the same time. In this method, a student could simultaneously conduct genome editing experiment using 10 plasmids targeting different genome positions and finally obtained all the corresponding transformants with target DNA knocked out, indicating that A. rhizogenes-mediated genome editing technology is highly efficient. In addition, A. rhizogenes can be used for direct viral vector inoculation on citrus bypassing the step of viron enrichment in tobacco, which facilitates the experiment operation of virus-induced gene silence (VIGS) and foreign gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus, which can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by removing high cost, heavy workload, long experiment period and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.

opencc-zeroDec 2021View details →

Oncorhynchus kisutch genetic stock ID SNP baseline

Genetic stock identification (GSI) using genotypes produced from genotyping-by-sequencing of SNP loci has become the gold standard for stock identification in Pacific salmon, which are found in mixed stocks in the ocean. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and promise real-time, in-field stock identification on variable batch sizes. Here we evaluate utility and comparability to established GSI platforms of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during a high-sea winter expedition to the Gulf of Alaska. As long read sequencers are not optimized for short amplicons, we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach by providing mobile small batch genotyping to diverse stakeholders.

opencc-zeroJan 2022View details →

Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections

The interior Southeastern United States could contain novel germplasm for the bioenergy crop switchgrass due to its diverse habitats and geographic location between genetic subpopulations (Atlantic, Midwest, and Gulf). Collections from this region could accelerate breeding progress, contribute to conservation efforts, and improve understanding of isolated grasslands in the region. This study located 22 sites in the Midsouth region and obtained 1,521,210 single nucleotide polymorphism markers of 202 individuals through genotype-by-sequencing. Individuals were evaluated for flowering time, winter survival and tiller number. Comparison to a national diversity panel revealed that branches of two major subpopulations occur in the region with two levels of polyploidy: Atlantic tetraploids and Midwest octoploids. Two locations contained admixed octoploid individuals with Midwest and Gulf genetics. Field performance of the Midwest octoploids conformed with prior reported performance of the Midwest subpopulation, although three sites contained promising late flowering traits. The Atlantic tetraploids had moderate winter survival, short stature, and anomalously early flowering. Atlantic populations mostly occurred in marginal sites and their morphological and flowering time adaptations may be a resource conservation strategy. Demographic inference of historical effective population size variation in a subset of tetraploid locations indicated a widespread recent decline in effective population size. This pattern is consistent with isolation of these switchgrass communities from larger populations and is further supported by evidence of inbreeding within the populations (FI = 0.18). The populations documented in this study contain novel genetic diversity and adaptations to a range of marginal habitats. Therefore, this study provides a new source of germplasm for future breeding and conservation programs.

opencc-zeroJan 2022View details →

Heterogeneous genetic structure in eastern North American peatmosses (Sphagnum)

Bryophytes generally have broad geographic ranges that suggest high dispersal ability. The aim of this study was to test hypotheses about dispersal limitation, as indicated by isolation by distance (IBD), in four spore producing species of the moss genus Sphagnum (S. carolinianum, S. missouricum, S. macrophyllum, S. pylaesii), and to assess whether plants in the southern United States harbor high levels of unique alleles and/or other indicators of exceptional genetic diversity. IBD was detected in all four species, but regional patterns of genetic structure were very species-specific. One species, S. macrophyllum, exhibited differentiation between northern and southern genetic groups that appear to reflect more ancient phylogenetic diversification.

opencc-zeroJan 2022View details →

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica as one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (NST > GST, p > 0.05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plots (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period, and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.

Linking genetic diversity and species diversity through plant-soil feedback

Genetic diversity and species diversity are typically studied in isolation despite theory showing they likely influence one another. Here, we used simplified communities of one or two populations of one or two species to test whether linkages between genetic and species diversity can be mediated by interactions between plants and their soil microbiota, or microbe-mediated plant-soil feedback (PSF). Interspecific PSF promotes the maintenance of species diversity when plants grow better with heterospecific soil microbes than with conspecific microbes. Similarly, intraspecific PSF promotes the maintenance of genetic diversity when plants grow better with heterogenotypic than with congenotypic microbes. In a two-generation greenhouse experiment, we conditioned the soil microbial community with pairs of plants that were either two individuals of the same species (lower species diversity) or one individual of each of two species (higher species diversity), and with pairs of plants that were either two individuals from the same population (lower genetic diversity) or one individual from each of two populations (higher genetic diversity). We then tested the effects of these microbial communities on plant growth in a second generation. We found that higher genetic diversity reduced the ability of interspecific PSF to promote plant species diversity, and for one of our two study species, higher species diversity reduced the ability of intraspecific PSF to promote plant genetic diversity. If these patterns occur in more diverse communities, then our results suggest that PSF may dampen the negative effects of diversity loss by promoting diversity at other levels of biological organization.

Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)

Hybridization with introduced or invasive species is a major threat and driver of population declines in native salmonids. The rainbow trout (Oncorhynchus mykiss, RBT) has been widely introduced globally and represents an important invasive species, often establishing entrenched naturalized populations. The cutthroat trout (Oncorhynchus clarkii, CT), a close congener, is particularly susceptible to competition and hybridization from RBT introductions which has led to range-wide population declines and loss of CT genetic variation. The Lahontan CT (O. c. henshawi, LCT) whose historic distribution included the Lake Tahoe basin, was extirpated by the 1940s due to overfishing and introduction of nonnative salmonids, including now naturalized RBT. Here, we characterize genetic variation of RBT in a subset of Lake Tahoe tributaries to assess potential homing of RBT to streams for spawning, thereby informing LCT reintroduction. Diploid reproductively viable RBT were stocked annually into Lake Tahoe from the late 1800s until the mid-2000s by California and Nevada fish and wildlife agencies, planting the same commonly raised hatchery strains over time. Since 2007, triploid RBT comprise the bulk of RBT planted. Despite extensive dispersal from stocking locations, our analyses revealed variation in population differentiation among tributaries, with individuals from spatially proximate streams clustering across multiple population genetic analyses. Although subtle, we detected evidence for genetic differentiation among tributaries from the southern, western, and northern regions, including surprising structure involving a single tributary. These results illustrate the extent of differentiation within and among streams and could inform possibilities for and implications of RBT removal and LCT reintroduction.

Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)

Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. Dracocephalum ruyschiana is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for D. ruyschiana, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of D. ruyschiana. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.

Genetic data disagree with described subspecies ranges for Seaside Sparrows on the Atlantic coast

Seaside Sparrows (Ammospiza maritima) are tidal salt marsh endemic passerines found along the Atlantic and Gulf coasts of North America. Currently there are 7 described subspecies and "MacGillivray's" Seaside Sparrow (A. m. macgillivraii) is the name given to the Atlantic coast subspecies breeding from North Carolina to northern Florida. In 2019 the US Fish and Wildlife Service received a petition to list this subspecies under the Endangered Species Act due to shrinking populations and loss of marsh habitat, which necessitated a Species Status Assessment. As part of the Species Status Assessment, we analyzed genetic (microsatellite and mitochondria) data from 464 Seaside Sparrows from Connecticut to Florida, USA, to infer population connectivity (gene flow) among Atlantic coast populations, and to assess the concordance of population genetic data with the putative ranges of the subspecies. Bayesian cluster analysis (program Structure) indicates three genetically distinct population segments that were recovered: (1) Florida + Georgia, (2) Charleston, South Carolina, and (3) North Carolina to Connecticut. The population in Charleston, South Carolina was the most strongly differentiated based on microsatellite data, and harbored a unique mitochondrial haplotype not shared by other sampling locations, possibly reflecting long-standing isolation. Our results indicate population genetic discordance with currently described ranges of the subspecies of Seaside Sparrow and provide grounds for the consideration of separate management plans for the three populations.

opencc-by-4.0Jan 2022View details →

Population genetics reveal that the western Tianshan Mountains populations of Agrilus mali (Coleoptera: Buprestidae) may not be introduced recently

Supplementary charts and haplotype sequences for all genes in the article are included in this zip file.

Datasets for manuscript: The nature, representation and measure of genetic information

Current studies in genetics very often refer to notions from information science. The concept of genetic information is still disputed because it attributes semantic traits to what seem to be regular biochemical entities. Some researchers maintain that the use of information in biology is just metaphorical and maybe even misleading. In this paper, we offer an analysis of the nature and characteristics of the use of information in proteins, protein families, and their sequences. It is argued that the foundation of the metaphorical view is relatively weak given the current findings in bioinformatics, and it is shown that the present understanding of genetics fits well into the context of the modern philosophy of information. Here, we propose an extension of Floridi's conceptual model of information to include genetic information better. In addition, we discuss how to understand the qualitative aspects of genetic information and how to measure its quantitative aspects and present a joint statistical model including qualitative genetics, where the nominal genetic function is represented jointly with its metric self-information. The functional information of protein families in the Cath and Pfam databases are analysed. The paper concludes that scientific work may place information firmly as one of the fundamental components of molecular biology. The protein alignment files from the Cath and Pfam databases are in FASTA format.

opencc-zeroDec 2010View details →

Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population

Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.

Data from: RNA-Seq reveals adaptive genetic potential of the rare Torrey pine (Pinus torreyana) in the face of Ips bark beetle outbreaks

The ability of tree species to adapt to water stress and increased frequency of bark beetle outbreaks with climate change may increase with population size and standing genetic variation, calling into question the resilience of small, rare plant populations. The Torrey pine (Pinus torreyana) is a rare, genetically depauperate conifer that occurs naturally in a mainland and island population in southern California. Due to recent declines in the mainland population coinciding with drought and Ips paraconfusus bark beetle outbreaks, the species would benefit from an assessment of adaptive genetic diversity. Here, we use RNA-Seq to survey gene-coding diversity across 40 individuals to 1) characterize patterns of genetic diversity in the species and 2) test for genetic differentiation between trees that succumbed to beetle attack or survived following an outbreak. Consistent with previous studies, we found few genetic variants, with most SNPs occurring as fixed differences between populations. However, we found structure within the mainland and polymorphisms segregating in both populations. Interestingly, we found differentiation in genotypes between attacked and surviving trees and 11 SNPs associated with survival status, several of which had defense-related functions. While low diversity suggests limited adaptive capacity, genetic associations with survival in functionally relevant genes suggest adaptive potential for bark beetle defense. This initial study prompts future research to explore the genetic basis of putative resistance and suggests conservation efforts should protect surviving genotypes and the full spectrum of genetic diversity across populations to preserve the evolutionary potential of the species.

opencc-zeroMar 2022View details →

Data from: The genetic basis of variation in sexual aggression: evolution versus social plasticity

Male sexual aggression towards females is a form of sexual conflict that can result in increased fitness for males through forced copulations or coercive matings at the cost of female lifetime fitness. We used male fruit flies (Drosophila melanogaster) as a model system to uncover the genomic contributions to variation in forced copulation, both due to standing variation in a wild population, and due to plastic changes associated with variation in social experience. We used RNAseq to analyze whole-transcriptome differential expression in male head tissue associated with evolved changes in forced copulation from lineages previously selected for high and low forced copulation rate (Dukas et al., 2020), and in male flies with varying forced copulation rates due to social experience. We identified hundreds of genes associated with evolved and plastic variation in forced copulation, however only a small proportion (27 genes) showed consistent differential expression due to both modes of variation. We confirmed this trend of low concordance in gene expression effects across broader sets of genes significant in either the evolved or plastic analyses using multivariate approaches. The gene ontology terms neuropeptide hormone activity and serotonin receptor activity were significantly enriched in the set of significant genes. Of 7 genes chosen for RNAi knockdown validation tests, knockdowns of 4 genes showed the expected effect on forced copulation behaviours. Taken together, our results provide important information about the apparently independent genetic architectures that underlie natural variation in sexual aggression due to evolution and plasticity.

opencc-zeroMar 2022View details →

Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (approximately 1000 ind.), suggesting that the evolutionary potential of the species is not assured.

FIGURE 11 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)

FIGURE 11. Zephronia chrysomallos Bhansali & Wesener sp. nov., holotype ♂ (NHMD MYR8826), drawings, A. Left posterior telopod, anterior view. B. Left posterior telopod, posterior view. Abbreviations: ct = crenulated teeth; imf = immovable finger; ss = sclerotized spot. Scale bars = 1 mm.

FIGURE 12 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)

FIGURE 12. Zephronia erawani Bhansali & Wesener sp. nov., holotype ♂ (NHMD K56-9), volume rendering based on microcomputed tomography. A. Habitus, lateral view. B. Habitus, ventro-lateral view. C. Habitus, ventral view. D. Habitus, anterior view. E. Body-ring architecture, cross section trough midbody-ring. Abbreviations: Ant = Antennae; As = anal shield; Cl = clypeus; Col = collum; Cp = central pad; Cx = coxa; Fe = femur; Gc = gnathochilarium; Go = gonopore; Ip = inner palpi; Lc = locking carina; o = ommatidia; Pl = pleurite; Pl1= pleurite 1; Pl2= pleurite 2; Po = postfemur; Pre = prefemur; Pt = paratergite; Stp = stigmatic plate; St = stipites; Ta = tarsus; Te = tergite; Tg = thoracic shield groove; Ti = tibia; Ts = thoracic shield. Not to scale.

FIGURE 8 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)

FIGURE 8. Zephronia chrysomallos Bhansali & Wesener sp. nov., holotype ♂ (ZFMK MYR8826), scanning electron micrographs. A. Left antennae, lateral view. B. Left sixth antennomere with antennal disc. C. Left antenna, disc. D. Gnathochilarium, apical view. E. Left lateral palpi. F. Left central pad, two types of sensory cones on central pad, detail. Abbreviations: ac = apical cone; ad = antennal disc; Cp = central pad; Hyp = hypopharynx; Ip = inner palpi; LL = lamellae lingulales; Sc = sensory cone; St = stipites.

FIGURE 7 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)

FIGURE 7. Zephronia chrysomallos Bhansali & Wesener sp. nov., paratype ♂ (ZFMK MYR11366), volume rendering based on micro-computed tomography. A. Habitus, lateral view. B. Habitus, ventro-lateral view. C. Habitus, ventral view. D. Habitus, anterior view. E. Body-ring architecture, cross section trough midbody-ring. Abbreviations: Ant = Antennae; As = anal shield; Cl = clypeus; Col = collum; Cx = coxa; Fe = femur; Gc = gnathochilarium; Go = gonopore; Ip = inner palpi; Lc = locking carina; O = ommatidia; Pl = pleurite; Pl1= pleurite 1; Pl2= pleurite 2; Pre = prefemur; Pt = paratergite; St = stigmatic plate; Ta = tarsus; Te = tergite; Tg = thoracic shield groove; Ti = tibia; Tr = tracheal apodeme; Ts = thoracic shield. Not to scale.

FIGURE 5 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)

FIGURE 5. Sphaerobelum meridionalis Bhansali & Wesener sp. nov., holotype ♂ (MHNG 4B-2), drawings, A. Left posterior telopod, anterior view. B. Left posterior telopod, posterior view. Abbreviations: ct = crenulated teeth; imf = immovable finger; ms = membranous spot; ss = sclerotized spot. Scale bars = 1 mm.