The evolutionary landscape of the Rab family in chordates

Abstract

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The Cis-Regulatory Code for Kelch-like 21/30 Specific Expression in Ciona robusta Sensory Organs

“…In contrast, C. robusta retained 32 Klhl genes and 16 subfamilies, whilst O. dioica maintained 14 genes and 10 subfamilies. This is coherent to the tendency of the fast-evolving Oikopleura dioica to lose large portions of gene families (Berná and Alvarez-Valin, 2014;Albalat and Cañestro, 2016;Martí-Solans et al, 2016;Coppola et al, 2019). Otherwise, we also detected different tunicate-specific duplications of certain Kelch-like genes in either species (Figure 1).…”

Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta

“…The concept of orthology among invertebrate Rimbp, Rimbp2, and Rimbp3 genes is enforced by the synteny we found between human RIMBP3A and Rimbp of ascidians (Figure S2). Moreover, a strong phylogenetic signal proved that Rimbp genes are preserved in all the surveyed tunicates (Figures 1 and S2), despite these animals had undergone massive gene losses [51,52], suggesting an essential role for Rimbp.…”

Origin and evolutionary landscape of Nr2f transcription factors across Metazoa

“…Importantly, our data support a model in which a single Nr2f gene (Nr2f1/2/5/6), which is present in extant cnidarians and placozoans, predated the six Bilateria subfamilies that include Nr2f1/2/5 (found in invertebrates), Nr2f1/5 (found in agnathans), and Nr2f1, Nr2f2, Nr2f5, and Nr2f6 (found in vertebrates; Fig 9). Single, conserved Nr2f1/2/5 genes are predominantly found throughout invertebrate protostomes and deuterostomes and have even been retained in species traditionally considered gene losers, such as the tunicates [42,51,52]. There has been significant expansion and retention of Nr2fs in gnathostomes, particularly in teleosts.…”

“…To complement the phylogenetic analysis of Nr2f genes, we first analyzed the conservation of Nr2f intron/exon structure [40][41][42]. Intron/exon junctions from earlybranching metazoans and vertebrates matching the transcripts and the translated proteins were mapped and given a score for the intron phases (S1 File), with 0, 1 and 2 introns falling before the first, second and third bases of a codon, respectively.…”

“…Gene structures were deduced after merging the genomic sequences with ESTs when available, as previously described [40][41][42]. Introns were classified as phase 0, phase 1, and phase 2, according to their positions with respect to the protein-reading frame.…”