| 1. |
- Ahola, Virpi, et al.
(author)
-
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
- 2014
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4737-
-
Journal article (peer-reviewed)abstract
- Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
|
|
| 2. |
- Celorio-Mancera, Maria de la Paz, et al.
(author)
-
Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)
- 2021
-
In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653 .- 1759-6653. ; 13:5
-
Journal article (peer-reviewed)abstract
- The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.
|
|
| 3. |
- Fountain, Toby, et al.
(author)
-
Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly
- 2018
-
In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 11:3, s. 287-297
-
Journal article (peer-reviewed)abstract
- Dispersal is important for determining both species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville fritillary butterfly (Melitaea cinxia L.), in the Åland Islands in SW Finland. This is an ideal system to test the effectiveness of this approach due to the wealth of information already available covering dispersal across small spatial and temporal scales, but lack of information at larger spatial and temporal scales. We sampled three larvae per larval family group from 3732 groups over a six-year period and genotyped for 272 SNPs across the genome. We used this empirical data set to reconstruct cases where full-sibs were detected in different local populations to infer female effective dispersal distance, that is, dispersal events directly contributing to gene flow. On average this was one kilometre, closely matching previous dispersal estimates made using direct observation. To evaluate our power to detect full-sib families, we performed forward simulations using an individual-based model constructed and parameterized for the Glanville fritillary metapopulation. Using these simulations, 100% of predicted full-sibs were correct and over 98% of all true full-sib pairs were detected. We therefore demonstrate that even in a highly dynamic system with a relatively small number of markers, we can accurately reconstruct full-sib families and for the first time make inferences on female effective dispersal. This highlights the utility of this approach in systems where it has previously been impossible to obtain accurate estimates of dispersal over both ecological and evolutionary scales.
|
|
| 4. |
- Hill, Jason, et al.
(author)
-
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution
- 2019
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:6
-
Journal article (peer-reviewed)abstract
- Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
|
|
| 5. |
- Salojarvi, Jarkko, et al.
(author)
-
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
- 2017
-
In: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 49:6, s. 904-912
-
Journal article (peer-reviewed)abstract
- Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.
|
|
| 6. |
- Smolander, Olli Pekka, et al.
(author)
-
Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
- 2022
-
In: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 11
-
Journal article (peer-reviewed)abstract
- Background: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.
|
|
| 7. |
- Tunström, Kalle, 1991-, et al.
(author)
-
Evidence for a single, ancient origin of a genus-wide alternative life history strategy
- 2023
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 9:12
-
Journal article (peer-reviewed)abstract
- Understanding the evolutionary origins and factors maintaining alternative life history strategies (ALHS) within species is a major goal of evolutionary research. While alternative alleles causing discrete ALHS are expected to purge or fix over time, one-third of the ~90 species of Colias butterflies are polymorphic for a female-limited ALHS called Alba. Whether Alba arose once, evolved in parallel, or has been exchanged among taxa is currently unknown. Using comparative genome-wide association study (GWAS) and population genomic analyses, we placed the genetic basis of Alba in time-calibrated phylogenomic framework, revealing that Alba evolved once near the base of the genus and has been subsequently maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was then used to verify a putative cis-regulatory region of Alba, which we identified using phylogenetic foot printing. We hypothesize that this cis-regulatory region acts as a modular enhancer for the induction of the Alba ALHS, which has likely facilitated its long evolutionary persistence.
|
|
