Chromosomal and DNA barcode analysis of the Melitaea ala Staudinger, 1881 species complex (Lepidoptera, Nymphalidae)

The species of the Melitaea ala Staudinger, 1881 complex are distributed in Central Asia. Here we show that this complex is a monophyletic group including the species, M. ala, M. kotshubeji Sheljuzhko, 1929 and M. enarea Fruhstorfer, 1917. The haploid chromosome number n=29 is found in M. ala and M. kotshubeji and is, most likely, a symplesiomorphy of the M. ala complex. We show that M. ala consists of four subspecies: M. ala zaisana Lukhtanov, 1999 (=M. ala irtyshica Lukhtanov, 1999, syn. nov.) (South Altai, Zaisan Lake valley), M. ala ala (Dzhungarian Alatau), M. ala bicolor Seitz, 1908 (North, East, Central and West Tian-Shan) and M. ala determinata Bryk, 1940 (described from “Fu-Shu-Shi”, China). We demonstrate that M. kotshubeji kotshubeji (Peter the Great Mts in Tajikistan) and M. kotshubeji bundeli Kolesnichenko, 1999 (Alai Mts in Tajikistan and Kyrgyzstan) are distinct taxa despite their geographic proximity in East Tajikistan. Melitaea enarea is widely distributed in the southern part of Central Asia and is sympatric with M. kotshubeji.

Comparative Cytogenetic Analysis of Three Eumeninae Species (Hymenoptera, Vespidae)

Eumeninae represents the largest subfamily within Vespidae, with 3,600 species described. Of these, only 18 have been cytogenetically analysed. In the present study, we used both classical and molecular techniques to characterise and compare the karyotypes of 3 Eumeninae species, namely, <i>Ancistrocerus</i> sp., <i>Pachodynerus grandis,</i> and <i>Pachodynerus nasidens</i>. <i>Ancistrocerus</i> sp. presented a haploid chromosome number of n = 12, with the first 2 chromosomes of the karyotype being almost entirely heterochromatic and much larger than the remaining chromosomes. The 2 <i>Pachodynerus</i> species presented the same chromosome number (n = 11 and 2n = 22) but displayed different karyotypic formulae<i>.</i> Additionally, chromosomal polymorphisms were observed in the analysed <i>P. nasidens</i> female. In the 3 species, heterochromatin was located in one of the chromosome arms. Fluorochrome staining revealed a balanced composition of AT and GC bases within the chromatin for each of the 3 species, except for few regions that were visibly GC-rich. All species had a single 18S rDNA site that co-localised with GC-rich regions; however, this localisation varied from species to species and not all GC-rich regions corresponded to ribosomal genes. Based on the cytogenetic data obtained here, we discuss the possible numerical/structural rearrangements that may be involved in the karyotypic evolution of the 3 studied species. In addition to the first description of the molecular cytogenetic characteristics of the Eumeninae subfamily and the genus <i>Pachodynerus</i>, this study also provides a relevant contribution towards the discussion of chromosomal evolution in Eumeninae wasps.

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

Chromosomal and DNA barcode analysis of the Polyommatus (Agrodiaetus) damone (Eversmann, 1841) species complex (Lepidoptera, Lycaenidae)

The Polyommatus (Agrodiaetus) damone (Eversmann, 1841) species complex comprises from 5 to 8 species distributed in southeastern Europe and southern Siberia. Here we used chromosomal and DNA-barcode markers in order to test the taxonomic hypotheses previously suggested for this complex. We revealed that all taxa within this group demonstrate chromosomal stasis and share the same or very similar haploid chromosome number (n = 66 or n = 67). This finding is unexpected since the karyotypes are known to be very diverse and species-specific within the other taxa of the subgenus Agrodiaetus Hübner, 1822. Analysis of the mitochondrial gene COI revealed six diverged clusters of individuals within the complex. Each cluster has a specific geographic distribution and is characterized by distinct morphological features in the wing pattern. The clusters mostly (but not always) correlate with traditionally recognized species. As a result of our study, we describe a new subspecies P. (A.) iphigenides zarmitanussubsp. nov. from Uzbekistan and Tajikistan and show that the taxon originally described as Lycaena kindermanni var. melania Staudinger, 1886 represents a subspecies P. (A.) iphigenides melanius (Staudinger, 1886). Polyommatus (A.) samusi Korb, 2017 (syn. nov.) and P. (A.) melanius komarovi Korb, 2017 (syn. nov.) are considered here as junior subjective synonyms of P. (A.) iphigenides iphigenides (Staudinger, 1886).

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout

Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2N=64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.Article SummaryA de-novo genome assembly was generated for the Arlee homozygous line of rainbow trout to enable identification and characterization of genome variants towards developing a rainbow trout pan-genome reference. The new assembly was generated using the PacBio sequencing technology and scaffolding with Hi-C contact maps and Bionano optical mapping. A contiguous genome assembly was obtained, with the contig and scaffold N50 over 15.6 Mb and 39 Mb, respectively, and 95% of the assembly in chromosome sequences. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes.

Karyotype and DNA barcode of Polyommatus (Agrodiaetus) cyaneus (Staudinger, 1899) from its type locality: implication for taxonomic and evolutionary research in Polyommatus blue butterflies (Lepidoptera, Lycaenidae)

Chromosomal and molecular analyses of rapidly evolving organisms such as Polyommatus Latreille, 1804 blue butterflies are essential for understanding their taxonomy and evolutionary history, and the studies of populations from their type localities are crucially important for resolving problems of nomenclature and species identity. Here we present data on the topotypical population of the blue butterfly species described as Lycaena damone var. cyanea Staudinger, 1899. This taxon was described from Khankendi (Nagorno-Karabakh, Caucasus), and rediscovered at the type locality for the first time since it was collected there in 1869. The specimens were found on dry stony meadows with a predominance of Onobrychis radiata Bieberstein, 1810, on upper border of oak forests. Their haploid chromosome number (n) was established as n = 17. Chromosomal and mitochondrial DNA barcode analyses of the studied samples from type-locality provided an opportunity for the critical taxonomic re-examination of Caucasian species of the subgenus Agrodiaetus Hübner, 1822 of the genus Polyommatus Latreille, 1804. The obtained data support the interpretation of the P. (A.) cyaneus (Staudinger, 1899) and P. (A.) carmon (Herrich-Schäffer, 1851) as two different, not closely related species complexes as previously hypothesized by Hugo de Lesse. On the contrary, the treatment by Walter Forster who considered these taxa as two groups of conspecific populations was not supported by our data.

Karyotype and DNA barcode of Polyommatus (Agrodiaetus) cyaneus (Staudinger, 1899) from its type locality: implication for taxonomic and evolutionary research in Polyommatus blue butterflies (Lepidoptera, Lycaenidae)

Chromosomal and molecular analyses of rapidly evolving organisms such as Polyommatus Latreille, 1804 blue butterflies are essential for understanding their taxonomy and evolutionary history, and the studies of populations from their type localities are crucially important for resolving problems of nomenclature and species identity. Here we present data on the topotypical population of the blue butterfly species described as Lycaena damone var. cyanea Staudinger, 1899. This taxon was described from Khankendi (Nagorno-Karabakh, Caucasus), and rediscovered at the type locality for the first time since it was collected there in 1869. The specimens were found on dry stony meadows with a predominance of Onobrychis radiata Bieberstein, 1810, on upper border of oak forests. Their haploid chromosome number (n) was established as n = 17. Chromosomal and mitochondrial DNA barcode analyses of the studied samples from type-locality provided an opportunity for the critical taxonomic re-examination of Caucasian species of the subgenus Agrodiaetus Hübner, 1822 of the genus Polyommatus Latreille, 1804. The obtained data support the interpretation of the P. (A.) cyaneus (Staudinger, 1899) and P. (A.) carmon (Herrich-Schäffer, 1851) as two different, not closely related species complexes as previously hypothesized by Hugo de Lesse. On the contrary, the treatment by Walter Forster who considered these taxa as two groups of conspecific populations was not supported by our data.

Chromosomes of parasitic wasps of the superfamily Chalcidoidea (Hymenoptera): An overview

An overview of the current knowledge of chromosome sets of the parasitoid superfamily Chalcidoidea is given. Karyotypes of approximately 240 members of this group, i.e. just above one percent of described species, are studied up to now. Techniques for obtaining and analyzing preparations of chalcid chromosomes are outlined, including the so-called “traditional” and “modern” methods of differential staining as well as fluorescence in situ hybridization (FISH). Among the Chalcidoidea, the haploid chromosome number can vary from n = 3 to n = 11, with a clear mode at n = 6 and a second local maximum at n = 10. In this group, most chromosomes are either metacentric or submetacentric, but acrocentrics and/or subtelocentrics also can predominate, especially within karyotypes of certain Chalcidoidea with higher chromosome numbers. The following main types of chromosomal mutations are characteristic of chalcid karyotypes: inversions, fusions, translocations, polyploidy, aneuploidy and B chromosome variation. Although karyotype evolution of this superfamily was mainly studied using phylogenetic reconstructions based on morphological and/or molecular characters, chromosomal synapomorphies of certain groups were also revealed. Taxonomic implications of karyotypic features of the Chalcidoidea are apparently the most important at the species level, especially among cryptic taxa.

“Mind the Gap”: Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions

Globe artichoke (Cynara cardunculus var. scolymus; 2n2x=34) is cropped largely in the Mediterranean region, being Italy the leading world producer; however, over time, its cultivation has spread to the Americas and China. In 2016, we released the first (v1.0) globe artichoke genome sequence (http://www.artichokegenome.unito.it/). Its assembly was generated using ∼133-fold Illumina sequencing data, covering 725 of the 1,084 Mb genome, of which 526 Mb (73%) were anchored to 17 chromosomal pseudomolecules. Based on v1.0 sequencing data, we generated a new genome assembly (v2.0), obtained from a Hi-C (Dovetail) genomic library, and which improves the scaffold N50 from 126 kb to 44.8 Mb (∼356-fold increase) and N90 from 29 kb to 17.8 Mb (∼685-fold increase). While the L90 of the v1.0 sequence included 6,123 scaffolds, the new v2.0 just 15 super-scaffolds, a number close to the haploid chromosome number of the species. The newly generated super-scaffolds were assigned to pseudomolecules using reciprocal blast procedures. The cumulative size of unplaced scaffolds in v2.0 was reduced of 165 Mb, increasing to 94% the anchored genome sequence. The marked improvement is mainly attributable to the ability of the proximity ligation-based approach to deal with both heterochromatic (e.g.: peri-centromeric) and euchromatic regions during the assembly procedure, which allowed to physically locate low recombination regions. The new high-quality reference genome enhances the taxonomic breadth of the data available for comparative plant genomics and led to a new accurate gene prediction (28,632 genes), thus promoting the map-based cloning of economically important genes.

A deep dive into the ancestral chromosome number and genome size of flowering plants

SummaryChromosome number and genome variation in flowering plants has stimulated a blossoming number of speculations about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal.We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 thousands taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5 thousands taxa.Our inferences revealed an ancestral haploid chromosome number for angiosperms n = 7, a diploid status, and an ancestral 1C = 1.73 pg. For 160 families, inferred ancestral n are provided for the first time.Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, also 1C genome size significantly increases (or decreases) in late-branching lineages. Therefore, no evidence exists for a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.