In Memoriam: David L. Nanney (1925–2016)

Doerder, F. Paul; Frankel, Joseph

doi:10.1111/jeu.12374

Cited by 2 publications

(3 citation statements)

References 40 publications

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“…A species tree was inferred using phylogenomic analysis of 198 one-to-one ortholog genes identified in the 10 Tetrahymena species and in 5 other ciliate species used as outgroups: Ichthyophthirius multifiliis , Pseudocohnilembus persalinus , Paramecium tetraurelia , Oxytricha trifallax , and Stylonychia lemnae (Fig 1A). Molecular clock estimates of divergence times suggest that the Tetrahymena genus originated more than 300 million years ago (Mya) (Fig 1A), similar to previous estimates based on the rDNA sequences [13, 21]. This origin time is comparable to that of mammals and is far earlier than that of the Drosophila genus, approximately 40 Mya [22].…”

Section: Resultssupporting

confidence: 82%

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Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena

et al. 2019

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A morphospecies is defined as a taxonomic species based wholly on morphology, but often morphospecies consist of clusters of cryptic species that can be identified genetically or molecularly. The nature of the evolutionary novelty that accompanies speciation in a morphospecies is an intriguing question. Morphospecies are particularly common among ciliates, a group of unicellular eukaryotes that separates 2 kinds of nuclei—the silenced germline nucleus (micronucleus [MIC]) and the actively expressed somatic nucleus (macronucleus [MAC])—within a common cytoplasm. Because of their very similar morphologies, members of the Tetrahymena genus are considered a morphospecies. We explored the hidden genomic evolution within this genus by performing a comprehensive comparative analysis of the somatic genomes of 10 species and the germline genomes of 2 species of Tetrahymena . These species show high genetic divergence; phylogenomic analysis suggests that the genus originated about 300 million years ago (Mya). Seven universal protein domains are preferentially included among the species-specific (i.e., the youngest) Tetrahymena genes. In particular, leucine-rich repeat (LRR) genes make the largest contribution to the high level of genome divergence of the 10 species. LRR genes can be sorted into 3 different age groups. Parallel evolutionary trajectories have independently occurred among LRR genes in the different Tetrahymena species. Thousands of young LRR genes contain tandem arrays of exactly 90-bp exons. The introns separating these exons show a unique, extreme phase 2 bias, suggesting a clonal origin and successive expansions of 90-bp–exon LRR genes. Identifying LRR gene age groups allowed us to document a Tetrahymena intron length cycle. The youngest 90-bp exon LRR genes in T . thermophila are concentrated in pericentromeric and subtelomeric regions of the 5 micronuclear chromosomes, suggesting that these regions act as genome innovation centers. Copies of a Tetrahymena Long interspersed element (LINE)-like retrotransposon are very frequently found physically adjacent to 90-bp exon/intron repeat units of the youngest LRR genes. We propose that Tetrahymena species have used a massive exon-shuffling mechanism, involving unequal crossing over possibly in concert with retrotransposition, to create the unique 90-bp exon array LRR genes.

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Section: Resultssupporting

confidence: 82%

“…Nanney noted this phenomenon in Tetrahymena long ago [13, 21]. Based on the divergence of rDNA sequence, he estimated this genus has existed for approximately 300 million years although its morphological design has persisted unchanged [13, 21].…”

Section: Discussionmentioning

confidence: 99%