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1. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

   https://doi.org/10.1093/gbe/evae157  

   Gable, Simone M; Bushroe, Nicholas A; Mendez, Jasmine M; Wilson, Adam; Pinto, Brendan J; Gamble, Tony; Tollis, Marc (July 2024, Genome Biology and Evolution)

   Mueller, Rachel (Ed.)

   Abstract Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history. 

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2. Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates

   https://doi.org/10.1371/journal.pone.0291688  

   Maurer-Alcalá, Xyrus X; Cote-L’Heureux, Auden; Kosakovsky_Pond, Sergei L; Katz, Laura A (January 2024, PLOS ONE)

   Schmidt, Edward E (Ed.)

   The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution ofde novogenes in model species. Here we explore the origins of lineage-specific genes in ciliates, a ~1 billion year old clade of microeukaryotes that are defined by their division of somatic and germline functions into distinct nuclei. Previous analyses on conserved gene families have shown the effect of ciliates’ unusual genome architecture on gene family evolution: extensive genome processing–the generation of thousands of gene-sized somatic chromosomes from canonical germline chromosomes–is associated with larger and more diverse gene families. To further study the relationship between ciliate genome architecture and gene family evolution, we analyzed lineage specific gene families from a set of 46 transcriptomes and 12 genomes representing x species from eight ciliate classes. We assess how the evolution lineage-specific gene families occurs among four groups of ciliates: extensive fragmenters with gene-size somatic chromosomes, non-extensive fragmenters with “large’’ multi-gene somatic chromosomes, Heterotrichea with highly polyploid somatic genomes and Karyorelictea with ‘paradiploid’ somatic genomes. Our analyses demonstrate that: 1) most lineage-specific gene families are found at shallow taxonomic scales; 2) extensive genome processing (i.e., gene unscrambling) during development likely influences the size and number of young lineage-specific gene families; and 3) the influence of somatic genome architecture on molecular evolution is increasingly apparent in older gene families. Altogether, these data highlight the influences of genome architecture on the evolution of lineage-specific gene families in eukaryotes. 

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3. De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

   https://doi.org/10.1101/gr.279443.124  

   Bista, Basanta; González-Rodelas, Laura; Álvarez-González, Lucía; Wu, Zhi-qiang; Montiel, Eugenia E; Lee, Ling Sze; Badenhorst, Daleen B; Radhakrishnan, Srihari; Literman, Robert; Navarro-Dominguez, Beatriz; et al (October 2024, Genome Research)

   Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq:Apalone spinifera(ZZ/ZW, 2n= 66) andStaurotypus triporcatus(XX/XY, 2n= 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling inApalone(Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions inStaurotypus(Kinosternidae) andTrachemys scripta(Emydidae). Furthermore, we identified a chromosome folding pattern that enables “centromere–telomere interactions” previously undetected in turtles. The combined turtle pattern of “centromere–telomere interactions” (discovered here) plus “centromere clustering” (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome. 

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4. Immunogenetic diversity and transcriptomic response to fibropapillomatosis in Hawaiian green sea turtles

   https://doi.org/10.3354/esr01403  

   Adkins, JL; Martin, KR; Lynch, J; Banerjee, S; Allen, CD; Savage, AE; Chea, V; Rice, M; Jones, TT; Komoroske, LM (May 2025, Endangered Species Research)

   Sea turtles are one taxon of high conservation concern that encounter many pathogens, but their disease ecology is understudied, hindering our ability to predict impacts of disease on population viability. Fibropapillomatosis (FP) is a neoplastic tumor-forming disease that has been documented in all sea turtle species, with an especially high prevalence in green turtlesChelonia mydas.Here, we use Hawaiian green turtles (honu) as a study system to examine the roles of immunogenetic diversity and transcriptional modulation in sea turtle disease responses. Specifically, we quantified gene expression profiles associated with FP and characterized host diversity of major histocompatibility complex class I (MHCI) immune loci. We found 65 genes differentially expressed in blood between clinically healthy (n = 5) and FP-afflicted turtles (n = 5) with enriched biological processes of the innate immune system, aligned with expectations of reptilian immune systems and active disease resistance. Our results also suggest a role for disease tolerance in response to FP, as evidenced by enriched biological processes related to regulation of immune and metabolic homeostasis, increase in cellular detoxification, and increased tissue repair mechanisms. Honu (n = 89) had 23 unique MHCI alleles belonging to 3 distinct functional supertypes, but none were significantly associated with FP; this could be a result of intrinsic demographic properties of the population or reflect a lesser/differing role of the reptilian adaptive immune system. Our study advances the understanding of reptilian disease response and evolutionary mechanisms underlying immunogenetic diversity, both of which are important for promoting the adaptive potential of species vulnerable to extinction. 

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5. Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels

   Vegesna, R; Tomaszkiewicz, M; Ryder, OA; Campos-Sanchez, R; Medvedev, P; DeGiorgio, M; Makova, KD (May 2020, Genome biology and evolution)

   Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species—chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families’ expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes. 

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