Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle

Abstract

Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120–160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.

Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis

“…A recent study demonstrates ~113,000 noncoding elements that have been conserved between two distantly related cephalochordate species, Asymmetron lucayanum and Branchiostoma floridae (Yue et al, ). We performed two types of Vista analyses.…”

The ups and downs of amphioxus biology: a history

“…Recently, transcriptomics and genomics of Asymmetron lucayanum, the sister genus of the two other genera (Branchiostoma and Epigonichthys) have been published (Yue et al, 2014(Yue et al, , 2016. Comparisons between Asymmetron and Branchiostoma genomes showed that the two genera, even though they split about 128-160 mya, are about the right distance apart for comparisons of the non-coding regions to reveal functional elements such regulatory elements (Yue et al, 2016). This demonstrates remarkably slow evolution, which was confirmed by comparisons of about 430 gene groups, showing that amphioxus are evolving more slowly than the slowest-evolving vertebrate known, the elephant shark (Yue et al, 2014).…”

Whole‐Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand‐New Variant Dataset for Branchiostoma

“…For these reasons, amphioxi are considered to be intermediate between vertebrates and invertebrates, and thus, are widely used as a model organism to study the evolution of invertebrate and the origin of vertebrates [1][2][3][4][5][6]. Previous studies have found that amphioxi are extremely genetically diverse animals with high population heterozygosity [2,3,[7][8][9]. However, amphioxi still maintain extreme similarity in their phenotypic characteristics, despite the high rate of genetic polymorphisms.…”