For many years, parasitic B chromosomes have been considered genetically inert elements. Here we show the presence of ten protein-coding genes in the B chromosome of the grasshopper Eyprepocnemis plorans. Four of these genes (CIP2A, GTPB6, KIF20A, and MTG1) were complete in the B chromosome whereas the six remaining (CKAP2, CAP-G, HYI, MYCB2, SLIT and TOP2A) were truncated. Five of these genes (CIP2A, CKAP2, CAP-G, KIF20A, and MYCB2) were significantly up-regulated in B-carrying individuals, as expected if they were actively transcribed from the B chromosome. This conclusion is supported by three truncated genes (CKAP2, CAP-G and MYCB2) which showed up-regulation only in the regions being present in the B chromosome. Our results indicate that B chromosomes are not so silenced as was hitherto believed. Interestingly, the five active genes in the B chromosome code for functions related with cell division, which is the main arena where B chromosome destiny is played. This suggests that B chromosome evolutionary success can lie on its gene content.

Sex-determining mechanisms (SDMs) set an individual's sexual fate by its genotype (genotypic sex determination, GSD) or environmental factors like temperature (temperature- dependent sex determination, TSD), as in turtles where the GSD “trigger” remains unknown. SDMs co-evolve with turtle chromosome number, perhaps because fusions/fissions alter the relative position/regulation of sexual development genes. Here, we map 10 such genes via FISH onto metaphase chromosomes in 6 TSD and 6 GSD turtles for the first time. Results uncovered intrachromosomal rearrangements involving 3 genes across SDMs (Dax1, Fhl2, and Fgf9) and a chromosomal fusion linking 2 genes (Sf1 and Rspo1) in 1 chromosome in a TSD turtle (Pelomedusa subrufa) that locate to 2 chromosomes in all others. Notably, Sf1 and its repressor Foxl2 map to Apalone spinifera's ZW chromosomes but to a macro- (Foxl2) and a microautosome (Sf1) in other turtles potentially inducing SDM evolution. However, our phylogenetically informed analysis refutes Foxl2 (but not Sf1) as Apalone's master sex-determining gene. The absence of common TSD-specific or GSD-specific rearrangements underscores the independent evolutionary trajectories of turtle SDMs. Further comparative analyses using more genes from the sexual development network are warranted to inform genome evolution and its contribution to enigmatic turnovers of vertebrate sex determination.

Background and Aims Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis of satellite DNA (satDNA) to investigate possible evolutionary trends in satDNA sequence features; (2) to determine the relative contribution of satDNA and other repetitive DNAs to its large genome; and (3) to analyse whether the reproduction mode or phase alternation between long-lasting haploid and diploid stages influences satDNA abundance or divergence. • Methods We analysed the repetitive fraction of the genome of this species in three different populations (one comprised only of independent gametophytes) using Illumina sequencing and bioinformatic analysis with RepeatExplorer and satMiner. • Key Results The satellitome of V. speciosa is composed of 11 satDNA families, most of them showing a short repeat length and being A + T rich. Some satDNAs had complex repeats composed of sub-repeats, showing high similarity to shorter satDNAs. Three families had particular structural features and highly conserved motifs. SatDNA only amounts to approx. 0.4 % of its genome. Likewise, microsatellites do not represent more than 2 %, but transposable elements (TEs) represent approx. 50 % of the sporophytic genomes. We found high resemblance in satDNA abundance and divergence between both gametophyte and sporophyte samples from the same population and between populations. • Conclusions (1) Longer (and older) satellites in V. speciosa have a higher A + T content and evolve from shorter ones and, in some cases, microsatellites were a source of new satDNAs; (2) the satellitome does not explain the huge genome size in this species while TEs are the major repetitive component of the V. speciosa genome and mostly contribute to its large genome; and (3) reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.

Centromeres are chromosomal regions essential for coordinating chromosome segregation during cell division. While centromeres are defined by the presence of a centromere-specific histone H3 variant called CENP-A rather than a particular DNA sequence, they are typically embedded in repeat-dense and heterochromatic chromosomal genome regions. In many species, centromeres are associated with transposable elements but it is unclear if these elements are selfish and target centromeres for insertion or if they play a role in centromere specification and function. Here we use Drosophila melanogaster as a model to understand the evolution of centromere-associated transposable elements. G2/Jockey-3 is a non-LTR retroelement in the Jockey clade and the only sequence shared by all centromeres. We study the evolution of G2/Jockey-3 using short and long read population genomic data to infer insertion polymorphisms across the genome. We combine estimates of the age, frequency, and location of insertions to infer the evolutionary processes shaping G2/Jockey-3 and its association with the centromeres. We find that G2/Jockey-3 is an active retroelement that is targeted by the piRNA pathway. Our results suggest that G2-Jockey-3 is highly enriched in centromeres at least in part due to an insertion bias. We do not detect any signature of positive selection on any G2/Jockey-3 insertions that would suggest than individual insertions are favored by natural selection. Instead, we infer that most insertions are neutral or weakly deleterious both inside and outside of the centromeres. Therefore, G2/Jockey-3 evolution is consistent with it being a selfish genetic element that targets centromeres. We suspect targeting centromeres for insertion helps active retroelements like G2/Jockey-3 escape host defenses, as the unique centromeric chromatin may prevent targeting by the host silencing machinery. On the other hand, centromeric TEs insertions may be tolerated or even beneficial if they also contribute to the right transcriptional and chromatin environment. Thus, we suspect centromere-associated retroelements like G2/Jockey-3 reflect a balance between conflict and cooperation at the centromeres.

26 Supernumerary (B) chromosomes are dispensable genomic elements found in most 27 kinds of eukaryotic genomes. Many show drive mechanisms that give them an 28 advantage in transmission, but how they achieve it remains a mystery. The recent 29 finding of protein-coding genes in B chromosomes has opened the possibility that 30 their evolutionary success is based on their genetic content. Using a protocol based on 31 mapping genomic DNA Illumina reads from B-carrying and B-lacking individuals on 32 the coding sequences of de novo transcriptomes from the same individuals, we 33 identified 25 protein-coding genes in the B chromosome of the migratory locust, 15 of 34 which showed a full coding region. Remarkably, one of these genes (apc1) codes for 35 the large subunit of the Anaphase Promoting Complex or Cyclosome (APC/C), an E3 36 ubiquitin ligase involved in the metaphase-anaphase transition. Sequence comparison 37 of A and B chromosome gene paralogs showed that the latter show B-specific 38 nucleotide changes, neither of which putatively impairs protein function. These 39 nucleotide signatures allowed identifying B-derived transcripts in B-carrying 40 transcriptomes, and demonstrated that they show about similar frequency as 41 A-derived ones. Since B-carrying individuals show higher amounts of apc1 42 transcripts than B-lacking ones, the putatively higher amount of APC1 protein might 43 induce a faster metaphase-anaphase transition in spite of orientation of the two B 44 chromosome chromatids towards the same pole during metaphase, thus facilitating B 45 chromosome non-disjunction. Therefore, apc1 is the first protein-coding gene 46 uncovered in a B chromosome that might be responsible for B chromosome drive. 47 48 Significance Statement 49 The genome of the migratory locust harbors a parasitic chromosome that arose about 50 2 million years ago. It is widespread in natural populations from Asia, Africa, 51 Australia and Europe, i.e. all continents where this species lives. The secret for such 52 an extraordinary evolutionary success is unveiled in this report, as B chromosomes in 53 this species contain active protein-coding genes whose transcripts might interfere with 54 gene expression in the host genome (the A chromosomes), thus facilitating B 55 chromosome mitotic and meiotic drive to provide the transmission advantage which 56 grants its success. One of the B-chromosomal genes (apc1) codes for the large subunit 57 of the Anaphase Promoting Complex or Cyclosome (APC/C) whose expression might 58 provide a mechanistic explanation for B chromosome drive. 59 60 61After 112 years since they were uncovered (1), B chromosomes continue being an 62 enigmatic part of eukaryote genomes. They were first considered as merely 63 genetically inert passengers of eukaryote genomes (2), a view supported by others (3) 64 but criticized by those who argued that B chromosomes are beneficial (4) or parasitic 65 (5) elements. In fact, as in most cases of selfish genetic elements, phenotypic effects 66 of B chromosomes are usually...