Programmed loss of millions of base pairs from a vertebrate genome

Abstract

In general, the strict preservation of broad-scale structure is thought to be critical for maintaining the precisely tuned functionality of vertebrate genomes, although nearly all vertebrate species undergo a small number of programmed local rearrangements during development (e.g., remodeling of adaptive immune receptor loci). However, a limited number of metazoan species undergo much more extensive reorganizations as a normal feature of their development. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate, undergoes a dramatic remodeling of its genome, resulting in the elimination of hundreds of millions of base pairs (and at least one transcribed locus) from many somatic cell lineages during embryonic development. These studies reveal the highly dynamic nature of the lamprey genome and provide the first example of broad-scale programmed rearrangement of a definitively vertebrate genome. Understanding the mechanisms by which this vertebrate species regulates such extensive remodeling of its genome will provide invaluable insight into factors that can promote stability and change in vertebrate genomes.A few species are known to undergo extensive genomic rearrangements during the specification of different cell lineages [e.g., sciarid flies (1, 2), some copepods (3, 4), and some roundworms (5)] or nuclear lineages [e.g., ciliates (6, 7)] (8). These rearrangements result in the selective removal of repetitive sequences (9-11), entire chromosomes (5), or single-copy genes (12, 13). Notably, only one chordate group (hagfish) is thought to undergo similar large-scale rearrangements and possesses certain repetitive elements in its germline that undergo diminution in somatic tissues, sometimes exhibiting a reduction in chromosome number (9-11). The unique genome biologies of these organisms are fascinating because changes that are tightly regulated in these exceptional genomes are reminiscent of the dysregulated structural changes that give rise to cancers or other genomic disorders (14,15). In this context, developmentally regulated rearrangements hold great potential for studying the factors that promote genome stability and change in normally developing somatic cells and the means by which alterations in genome structure contribute to the differentiation of cell lineages (8).Here, we report new data that reveal extensive programmed genome rearrangement in the sea lamprey, an important model system for studying basal vertebrate biology. Several complementary lines of evidence indicate that hundreds of megabases of DNA are specifically removed from somatic cell lineages. Here, we demonstrate the existence of a specific DNA sequence (called Germ1) that is highly abundant in germline but substantially rarer in many, if not all, somatic tissues. Fluorescence in situ hybridization reveals that Germ1 is present at a high copy number on several chromosomes in meiotic germline but dramatically reduced in soma. Estimates of relative copy number indicate that the loss of Germ1 is tightly regulated an...

Evidence for at least six Hox clusters in the Japanese lamprey ( Lethenteron japonicum )

“…KF318001-KF318013). Because it is known that ∼20% of germ-line DNA is lost in the somatic tissues of lamprey resulting from a developmentally programmed genome rearrangement (19), the blood library was used only to ensure complete coverage of the lamprey Hox gene repertoire. A combination of ab initio and homology-based methods was used to predict genes.…”

“…Thus, these CNEs may represent part of the core set of cis-regulatory elements that were present in the common ancestor of vertebrates. genome of the sea lamprey has revealed the presence of two Hox clusters and eight other Hox genes that could not be assigned to any cluster (19). Interestingly, previous phylogenetic analysis of sea lamprey Hox genes had suggested that the Hox clusters of sea lamprey and gnathostomes arose from independent duplications and that the last common ancestor of cyclostomes and gnathostomes had a single Hox cluster (20).…”

The evolution of tenascins and fibronectin

“…The difference in the number of tenascin genes identified in the 2 species may be due to the fact that the genome of P. marinus was sequenced from DNA taken from adult liver prior to the remarkable finding that hundreds of millions of base pairs are deleted from somatic cell lineages during the course of lamprey embryogenesis. 39 Germ cells were used as a source of DNA for the genomic sequencing of Lethenteron japonicum, which may account for the presence of the second tenascin. Although initial studies concluded that the agnathan/gnathostome divergence occurred after the 2 rounds of genome duplication early in vertebrate evolution, 28,40 recent study of Hox genes in the Japanese lamprey has led to the suggestion that genome duplications may have occurred independently in the lamprey lineage.…”

Bioinformatic Characterization of Genes and Proteins Involved in Blood Clotting in Lampreys

“…Neither the 2012 assembly for the sea lamprey (Smith et al 2013) nor the 2013 assembly for the Japanese lamprey (Mehta et al 2013) fully meet the criterion, however. It should be emphasized that the missing data from the 2012 sea lamprey assembly are not because of programmed loss of DNA during development (Smith et al 2009). The main reason for the deficiency is because a large number of trace reads were omitted during the assembly process, mostly because of being considered repetitive DNA.…”