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1. Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues

   https://doi.org/10.1093/gbe/evaa068  

   Pasquesi, Giulia I; Perry, Blair W; Vandewege, Mike W; Ruggiero, Robert P; Schield, Drew R; Castoe, Todd A (May 2020, Genome Biology and Evolution)

   Pritham, Ellen (Ed.)

   Abstract Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance. 

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2. A Comprehensive Analysis of Fibrillar Collagens in Lamprey Suggests a Conserved Role in Vertebrate Musculoskeletal Evolution

   https://doi.org/10.3389/fcell.2022.809979  

   Root, Zachary D.; Allen, Cara; Gould, Claire; Brewer, Margaux; Jandzik, David; Medeiros, Daniel M. (February 2022, Frontiers in Cell and Developmental Biology)

   Vertebrates have distinct tissues which are not present in invertebrate chordates nor other metazoans. The rise of these tissues also coincided with at least one round of whole-genome duplication as well as a suite of lineage-specific segmental duplications. Understanding whether novel genes lead to the origin and diversification of novel cell types, therefore, is of great importance in vertebrate evolution. Here we were particularly interested in the evolution of the vertebrate musculoskeletal system, the muscles and connective tissues that support a diversity of body plans. A major component of the musculoskeletal extracellular matrix (ECM) is fibrillar collagens, a gene family which has been greatly expanded upon in vertebrates. We thus asked whether the repertoire of fibrillar collagens in vertebrates reflects differences in the musculoskeletal system. To test this, we explored the diversity of fibrillar collagens in lamprey, a jawless vertebrate which diverged from jawed vertebrates (gnathostomes) more than five hundred million years ago and has undergone its own gene duplications. Some of the principal components of vertebrate hyaline cartilage are the fibrillar collagens type II and XI, but their presence in cartilage development across all vertebrate taxa has been disputed. We particularly emphasized the characterization of genes in the lamprey hyaline cartilage, testing if its collagen repertoire was similar to that in gnathostomes. Overall, we discovered thirteen fibrillar collagens from all known gene subfamilies in lamprey and were able to identify several lineage-specific duplications. We found that, while the collagen loci have undergone rearrangement, the Clade A genes have remained linked with the hox clusters, a phenomenon also seen in gnathostomes. While the lamprey muscular tissue was largely similar to that seen in gnathostomes, we saw considerable differences in the larval lamprey skeletal tissue, with distinct collagen combinations pertaining to different cartilage types. Our gene expression analyses were unable to identify type II collagen in the sea lamprey hyaline cartilage nor any other fibrillar collagen during chondrogenesis at the stages observed, meaning that sea lamprey likely no longer require these genes during early cartilage development. Our findings suggest that fibrillar collagens were multifunctional across the musculoskeletal system in the last common ancestor of vertebrates and have been largely conserved, but these genes alone cannot explain the origin of novel cell types. 

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3. Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Coevolved Components of Plant Immunity and Drought Response

   https://doi.org/10.1105/tpc.19.00903  

   Baggs, Erin L.; Monroe, J. Grey; Thanki, Anil S.; O’Grady, Ruby; Schudoma, Christian; Haerty, Wilfried; Krasileva, Ksenia V. (May 2020, The Plant Cell)

   Abstract Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived molecules and activate downstream signaling pathways. We analyzed the variation in NLR gene copy number and identified plants with a low number of NLR genes relative to sister species. We specifically focused on four plants from two distinct lineages, one monocot lineage (Alismatales) and one eudicot lineage (Lentibulariaceae). In these lineages, the loss of NLR genes coincides with loss of the well-known downstream immune signaling complex ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)/PHYTOALEXIN DEFICIENT 4 (PAD4). We expanded our analysis across whole proteomes and found that other characterized immune genes were absent only in Lentibulariaceae and Alismatales. Additionally, we identified genes of unknown function that were convergently lost together with EDS1/PAD4 in five plant species. Gene expression analyses in Arabidopsis (Arabidopsis thaliana) and Oryza sativa revealed that several homologs of the candidates are differentially expressed during pathogen infection, drought, and abscisic acid treatment. Our analysis provides evolutionary evidence for the rewiring of plant immunity in some plant lineages, as well as the coevolution of the EDS1/PAD4 pathway and drought responses. 

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4. FoxP2 Expression in a Highly Vocal Teleost Fish with Comparisons to Tetrapods

   https://doi.org/10.1159/000487793  

   Pengra, Ian G.G.; Marchaterre, Margaret A.; Bass, Andrew H. (July 2018, Brain, Behavior and Evolution)

   null (Ed.)

   Motivated by studies of speech deficits in humans, several studies over the past two decades have investigated the potential role of a forkhead domain transcription factor, FoxP2, in the central control of acoustic signaling/vocalization among vertebrates. Comparative neuroanatomical studies that mainly include mammalian and avian species have mapped the distribution of FoxP2 expression in multiple brain regions that imply a greater functional significance beyond vocalization that might be shared broadly across vertebrate lineages. To date, reports for teleost fish have been limited in number and scope to nonvocal species. Here, we map the neuroanatomical distribution of FoxP2 mRNA expression in a highly vocal teleost, the plainfin midshipman (Porichthys notatus). We report an extensive overlap between FoxP2 expression and vocal, auditory, and steroid-signaling systems with robust expression at multiple sites in the telencephalon, the preoptic area, the diencephalon, and the midbrain. Label was far more restricted in the hindbrain though robust in one region of the reticular formation. A comparison with other teleosts and tetrapods suggests an evolutionarily conserved FoxP2 phenotype important to vocal-acoustic and, more broadly, sensorimotor function among vertebrates. 

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5. Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16?

   https://doi.org/10.1098/rspb.2021.0346  

   Itoigawa, Akihiro; Fierro, Fabrizio; Chaney, Morgan E.; Lauterbur, M. Elise; Hayakawa, Takashi; Tosi, Anthony J.; Niv, Masha Y.; Imai, Hiroo (April 2021, Proceedings of the Royal Society B: Biological Sciences)

   null (Ed.)

   Bitter taste facilitates the detection of potentially harmful substances and is perceived via bitter taste receptors (TAS2Rs) expressed on the tongue and oral cavity in vertebrates. In primates, TAS2R16 specifically recognizes β-glucosides, which are important in cyanogenic plants' use of cyanide as a feeding deterrent. In this study, we performed cell-based functional assays for investigating the sensitivity of TAS2R16 to β-glucosides in three species of bamboo lemurs ( Prolemur simus, Hapalemur aureus and H. griseus ), which primarily consume high-cyanide bamboo. TAS2R16 receptors from bamboo lemurs had lower sensitivity to β-glucosides, including cyanogenic glucosides, than that of the closely related ring-tailed lemur ( Lemur catta ). Ancestral reconstructions of TAS2R16 for the bamboo-lemur last common ancestor (LCA) and that of the Hapalemur LCA showed an intermediate sensitivity to β-glucosides between that of the ring-tailed lemurs and bamboo lemurs. Mutagenetic analyses revealed that P. simus and H. griseus had separate species - specific substitutions that led to reduced sensitivity. These results indicate that low sensitivity to β-glucosides at the cellular level—a potentially adaptive trait for feeding on cyanogenic bamboo—evolved independently after the Prolemur – Hapalemur split in each species. 

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