Preferential occupancy of R2 retroelements on the B chromosomes of the grasshopper Eyprepocnemis plorans

Satellitome of the Red Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae), the Most Diverse Among Insects

The red palm weevil, Rhynchophorus ferrugineus, is the most harmful species among those pests affecting palm trees. Its impact causes important economic losses around the World. Nevertheless, the genetic information of Rh. ferrugineus is very scarce. Last year, the first genome assembly was published including a rough description of its repeatome. However, no information has been added about one of the main components of repeated DNA, the satellite DNA. Herein, we presented the characterization of the satellitome of this important species that includes 112 satellite DNA families, the largest number in an insect genome. These satellite DNA families made up around 25% of the genome while the most abundant family, RferSat01-169, alone represented 20.4%. Chromosomal location of most abundant satellite DNA families performed by fluorescence in situ hybridization showed that all of them are dispersed in the euchromatin on all chromosomes but some of them are also specifically accumulated either on the pericentromeric heterochromatic regions of all chromosomes or on specific chromosomes. Finally, the transcription of satellitome families was analyzed through Rh. ferrugineus development. It was found that 55 out of 112 satellite DNA families showed transcription, some families seemed to be transcribed across all stages while a few appeared to be stage-specific, indicating a possible role of those satellite DNA sequences in the development of this species.

Out of patterns, the euchromatic B chromosome of the grasshopper Abracris flavolineata is not enriched in high-copy repeats

In addition to the normal set of standard (A) chromosomes, some eukaryote species harbor supernumerary (B) chromosomes. In most cases, B chromosomes show differential condensation with respect to A chromosomes and display dark C-bands of heterochromatin, and some of them are highly enriched in repetitive DNA. Here we perform a comprehensive NGS (next-generation sequencing) analysis of the repeatome in the grasshopper Abracris flavolineata aimed at uncovering the molecular composition and origin of its B chromosome. Our results have revealed that this B chromosome shows a DNA repeat content highly similar to the DNA repeat content observed for euchromatic (non-C-banded) regions of A chromosomes. Moreover, this B chromosome shows little enrichment for high-copy repeats, with only a few elements showing overabundance in B-carrying individuals compared to the 0B individuals. Consequently, the few satellite DNAs (satDNAs) mapping on the B chromosome were mostly restricted to its centromeric and telomeric regions, and they displayed much smaller bands than those observed on the A chromosomes. Our data support the intraspecific origin of the B chromosome from the longest autosome by misdivision, isochromosome formation, and additional restructuring, with accumulation of specific repeats in one or both B chromosome arms, yielding a submetacentric B. Finally, the absence of B-specific satDNAs, which are frequent in other species, along with its euchromatic nature, suggest that this B chromosome arose recently and might still be starting a heterochromatinization process. On this basis, it could be a good model to investigate the initial steps of B chromosome evolution.

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

BACKGROUND

One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis.

RESULTS

We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success.

CONCLUSIONS

This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.

The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses

Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call "B-omics". We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.

B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.

Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust

Repetitive DNA is a major component in most eukaryotic genomes but is ignored in most genome sequencing projects. Here, we report the quantitative composition in repetitive DNA for a supernumerary (B) chromosome, in the migratory locust (Locusta migratoria), by Illumina sequencing of genomic DNA from B-carrying and B-lacking individuals and DNA obtained from a microdissected B chromosome, as well as the physical mapping of some elements. B chromosome DNA of 94.9% was repetitive, in high contrast with the 64.1% of standard (A) chromosomes. B chromosomes are enriched in satellite DNA (satDNA) (65.2% of B-DNA), with a single satellite (LmiSat02-176) comprising 55% of the B. Six satDNAs were visualized by FISH on the B chromosome, and the only A chromosome carrying all these satellites was autosome 9, pointing to this chromosome, along with autosome 8 (which shares histone genes with the B) as putative ancestors of the B chromosome. We found several transposable elements (TEs) showing nucleotidic variation specific to B-carrying individuals, which was also present in B-carrying transcriptomes. Remarkably, an interstitial region of the B chromosome included a 17 kb chimera composed of 29 different TEs, suggesting reiterative TE insertion in this B chromosome region.

Comment on Schielzeth et al. (2014): "Genome size variation affects song attractiveness in grasshoppers: Evidence for sexual selection against large genomes"

Schielzeth et al. (2014) concluded that attractive grasshopper singers have significantly smaller genomes thus suggesting a possible role for sexual selection on genome size. Whereas this conclusion could still be conceivably valid, it is not supported by the data presented due to some technical flaws. In addition, the interpretation of the results, speculating on the possible presence of B chromosomes, is not justified.

Integration, Regulation, and Long-Term Stability of R2 Retrotransposons

R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5' end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.

Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.

B chromosomes showing active ribosomal RNA genes contribute insignificant amounts of rRNA in the grasshopper Eyprepocnemis plorans

The genetic inertness of supernumerary (B) chromosomes has recently been called into question after finding several cases of gene activity on them. The grasshopper Eyprepocnemis plorans harbors B chromosomes containing large amounts of ribosomal DNA (rDNA) units, some of which are eventually active, but the amount of rRNA transcripts contributed by B chromosomes, compared to those of the standard (A) chromosomes, is unknown. Here, we address this question by means of quantitative PCR (qPCR) for two different ITS2 amplicons, one coming from rDNA units located in both A and B chromosomes (ITS2(A+B)) and the other being specific to B chromosomes (ITS2(B)). We analyzed six body parts in nine males showing rDNA expression in their B chromosomes in the testis. Amplification of the ITS2(B) amplicon was successful in RNA extracted from all six body parts analyzed, but showed relative quantification (RQ) values four orders of magnitude lower than those obtained for the ITS(A+B) amplicon. RQ values differed significantly between body parts for the two amplicons, with testis, accessory gland and wing muscle showing threefold higher values than head, gastric cecum and hind leg. We conclude that the level of B-specific rDNA expression is extremely low even in individuals where B chromosome rDNA is not completely silenced. Bearing in mind that B chromosomes carry the largest rDNA cluster in the E. plorans genome, we also infer that the relative contribution of B chromosome rRNA genes to ribosome biogenesis is insignificant, at least in the body parts analyzed.