The evolution of haploid chromosome numbers in Meliponini

Insights from Melipona bicolor hybrid genome assembly: a stingless bee genome with chromosome-level scaffold

BACKGROUND

The highly eusocial stingless bees are crucial pollinators of native and agricultural ecosystems. Nevertheless, genomic studies within this bee tribe remain scarce. We present the genome assembly of the stingless bee Melipona bicolor. This bee is a remarkable exception to the typical single-queen colony structure, since in this species, multiple queens may coexist and share reproductive duties, resulting in genetically diverse colonies with weak kinship connections. As the only known genuinely polygynous bee, M. bicolor's genome provides a valuable resource for investigating sociality beyond kin selection.

RESULTS

The genome was assembled employing a hybrid approach combining short and long reads, resulting in 241 contigs spanning 259 Mb (N50 of 6.2 Mb and 97.5% complete BUSCOs). Comparative analyses shed light on some evolutionary aspects of stingless bee genomics, including multiple chromosomal rearrangements in Melipona. Additionally, we explored the evolution of venom genes in M. bicolor and other stingless bees, revealing that, apart from two genes, the conserved repertoire of venom components remains under purifying selection in this clade.

CONCLUSION

This study advances our understanding of stingless bee genomics, contributing to the conservation efforts of these vital pollinators and offering insights into the evolutionary mechanisms driving their unique adaptations.

Chromosome Evolution in the Genus Partamona (Apidae: Meliponini), with Comments on B Chromosome Origin

The genus Partamona includes 33 species of stingless bees, of which 11 were studied cytogenetically. The main goal of this study was to propose a hypothesis about chromosomal evolution in Partamona by combining molecular and cytogenetic data. Cytogenetic analyses were performed on 3 Partamona species. In addition, the molecular phylogeny included mitochondrial sequences of 11 species. Although the diploid number was constant within the genus, 2n = 34, B chromosomes were reported in 7 species. Cytogenetic data showed karyotypic variations related to chromosome morphology and the amount and distribution of heterochromatin and repetitive DNA. The molecular phylogenetic reconstruction corroborated the monophyly of the genus and separated the 2 clades (A and B). This separation was also observed in the cytogenetic data, in which species within each clade shared most of the cytogenetic characteristics. Furthermore, our data suggested that the B chromosome in the genus Partamona likely originated from a common ancestor of the species that have it in clade B and, through interspecific hybridization, it appeared only in Partamona rustica from clade A. Based on the above, Partamona is an interesting genus for further investigations using molecular mapping of B chromosomes as well as for broadening phylogenetic data.

Karyotype Diversity, Mode, and Tempo of the Chromosomal Evolution of Attina (Formicidae: Myrmicinae: Attini): Is There an Upper Limit to Chromosome Number?

Simple Summary

Ants are an important insect group that includes a considerable number of species. Along with this diversity in species, they also exhibit a wide variation in chromosome numbers, from 1 up to 60 chromosomes. DNA molecules can be counted in a specific stage of the cell life cycle and quantified. These DNA molecules are very tightly packed together with several proteins and are called chromosomes. Each species shows a specific number of chromosomes with different shapes and sizes, as well as different quantities of DNA. We can use such information (the number of chromosomes, shape of the chromosomes, and quantity of DNA) as morphological attributes to study evolution at the species level. In this study, we describe new karyotypes of several ant species. In addition, from previous studies, we have compiled all the available information regarding the chromosome number and DNA quantity in fungus-farming ant cells. Different processes, called rearrangements, can change chromosomes over time, producing new character states. Such states can be tracked, along with the species and groups of similar species, using their relationships to identify patterns. We use DNA sequences to reconstruct the relationships of fungus-farming ant species (molecular phylogeny). By comparing such phylogeny with the chromosome number and DNA quantity, we discuss the evolution of chromosomes and DNA quantity (or genome size), and the potential limits to these features across fungus-farming ants.

Abstract

Ants are an important insect group that exhibits considerable diversity in chromosome numbers. Some species show only one chromosome, as in the males of the Australian bulldog ant Myrmecia croslandi, while some have as many as 60 chromosomes, as in the males of the giant Neotropical ant Dinoponera lucida. Fungus-growing ants are a diverse group in the Neotropical ant fauna, engaged in a symbiotic relationship with a basidiomycete fungus, and are widely distributed from Nearctic to Neotropical regions. Despite their importance, new chromosome counts are scarcely reported, and the marked variation in chromosome number across species has been poorly studied under phylogenetic and genome evolutionary contexts. Here, we present the results of the cytogenetic examination of fungus-farming ants and compile the cytogenetic characteristics and genome size of the species studied to date to draw insights regarding the evolutionary paths of karyotype changes and diversity. These data are coupled with a fossil-calibrated phylogenetic tree to discuss the mode and tempo of chromosomal shifting, considering whether there is an upper limit for chromosome number and genome size in ants, using fungus-farming ants as a model study. We recognize that karyotypes are generally quite variable across fungus-farming ant phylogeny, mostly between genera, and are more numerically conservative within genera. A low chromosome number, between 10 and 12 chromosomes, seems to present a notable long-term evolutionary stasis (intermediate evolutionary stasis) in fungus-farming ants. All the genome size values were inside a limited spectrum below 1 pg. Eventual departures in genome size occurred with regard to the mean of 0.38 pg, indicating that there is a genome, and likely a chromosome, number upper limit.

Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera

Background

Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae).

Results

Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3–12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species.

Conclusions

Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07987-3.

Robertsonian rearrangements in Neotropical Meliponini karyotype evolution (Hymenoptera: Apidae: Meliponini)

Genome changes, evidenced through karyotype or nuclear genome size data, can result in reproductive isolation, diversification and speciation. The aim of this study was to understand how changes in the karyotype such as chromosome number and nuclear genome size accompanied the evolution of neotropical stingless bees, and to discuss these data in a phylogenetic context focusing on the karyotype evolution of this clade. We sampled 38 species representing the three Neotropical Meliponini groups; 35 for karyotype analyses and 16 for 1C value measurement. The chromosome number varied from 2n = 16 to 2n = 34, with distinct karyotypic formulae and the presence of a few polymorphisms, such as B chromosomes in one species and arm size differences between homologous chromosomes in two species. The mean 1C value varied from 0.31 pg to 0.92 pg. We associated empirical data on chromosome number and mean 1C value to highlight the importance of Robertsonian fusion rearrangements, leading to a decrease in chromosome number during the Neotropical Meliponini evolution. These data also allowed us to infer the independent heterochromatin amplification in several genera. Although less frequent, Melipona species with 2n = 22 represent evidence of Robertsonian fissions. We also pointed out the importance of chromosomal rearrangements that did not alter chromosome number, such as inversions and heterochromatin amplification.

Different Levels of Chromatin Condensation in Partamona chapadicola and Partamona nhambiquara (Hymenoptera, Apidae)

Studies in several organisms have contributed to the understanding of heterochromatin and its biological importance. In bees of the tribe Meliponini, the presence of chromosomes with totally heterochromatic arms has been attributed to the mechanism of karyotype evolution in which this group accumulated heterochromatin to maintain telomere stability after centric fission events. In the present study, the use of classical and molecular cytogenetic techniques as well as automated image analysis software for the description of the karyotypes of Partamonachapadicola and P. nhambiquara bee species revealed variability in the compaction and patterns of chromatin structure. Although both species have the same chromosome number as other species in the genus Partamona (2n = 34), C-banding and image analyses indicated the existence of chromosomes with 3 regions of different staining intensities, suggesting a chromatin structure with distinct patterns and characteristics. Repetitive DNA probes hybridized only in the euchromatic regions, whereas the regions with intermediate staining intensity did not show any hybridization signals. This suggests that these regions present features more similar to heterochromatin. Evidence of the existence of a chromatin class with intermediate condensation compared to euchromatin and heterochromatin indicates a potential mechanism for heterochromatin amplification and demonstrates the need for further studies on this topic. This previously unrecognized class of chromatin should be taken into account in the study of all Meliponini chromosomes.