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Evolutionary history of LINE-1 in the major clades of placental mammals.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ - PLoS ONE (2007)

Bottom Line: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics.Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up.Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.

ABSTRACT

Background: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.

Methodology: To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.

Principal findings: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis.

Significance: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

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Related in: MedlinePlus

Phylogenetic tree of LINE-1: combined dataset. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our concatenated dataset (69 long and 109 short sequences; see text for details). Posterior probability values ≥95% are shown. Species in blue reflect sequences that are 1050 bp in length, whereas those in black correspond to the 300 bp sequences. Grey branches indicate sequences with >98% homology in their respective genomes. For species lacking whole genome sequencing projects, that is manatee, hyrax, golden mole, sloth, bat, among others, yellow is used to indicate pairs of sequences with >98% homology. This yields a minimum estimate of the number of copies of potentially recently active L1 in these species. A species key shows the abbreviated names, scientific names and common names. The tree is broken into two sections. The inset shows which part of the tree is displayed.
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pone-0000158-g001: Phylogenetic tree of LINE-1: combined dataset. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our concatenated dataset (69 long and 109 short sequences; see text for details). Posterior probability values ≥95% are shown. Species in blue reflect sequences that are 1050 bp in length, whereas those in black correspond to the 300 bp sequences. Grey branches indicate sequences with >98% homology in their respective genomes. For species lacking whole genome sequencing projects, that is manatee, hyrax, golden mole, sloth, bat, among others, yellow is used to indicate pairs of sequences with >98% homology. This yields a minimum estimate of the number of copies of potentially recently active L1 in these species. A species key shows the abbreviated names, scientific names and common names. The tree is broken into two sections. The inset shows which part of the tree is displayed.

Mentions: Since most LINE-1 copies are 5′-truncated and subsequently evolve as pseudogenes [1] they accumulate open reading frame (ORF) terminating, nonsense, and indel mutations. As expected, most of the 52 clones sequenced herein exhibit gaps and are non-active elements. Overall, five aardvark, three golden mole, one elephant and one bat clone displayed an ORF. It is probable that these represent a recent class of transposon not having had sufficient time to acquire mutations in this region. To further determine which lineages appeared recently active, all elements from the extended dataset were BLASTed against their genome of origin, and any that gave full-length hits with homologies higher than 98% have their branches coloured grey in Figure 1. A divergence of 2% is approximately 5 million years at the relatively slow rate that apes (e.g., chimp, human) evolve, or ∼1–3 million years for murid rodents which show the most rapid rates of change (along with tenrec) on our trees. These blast searches can of course be done only in those species for which there are at least whole genome shotgun sequence data (armadillo, elephant, tenrec, human, chimp, macaque, rabbit, mouse, rat, cow, dog). Therefore, to estimate recent activity in the absence of these data (for Cape serotine bat, aardvark, Cape golden mole, Cape elephant shrew, Cape rock hyrax, Cowan's shrew tenrec, Florida manatee, six-banded armadillo, tree anteater, pale-throated three-toed sloth), pairwise distances of closely related LINE-1 were checked, and any pair of sequences that were >98% similar to each other are coloured yellow in the tree (Figure 1). This gives a reasonable estimate of recently active LINE-1 in our dataset.


Evolutionary history of LINE-1 in the major clades of placental mammals.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ - PLoS ONE (2007)

Phylogenetic tree of LINE-1: combined dataset. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our concatenated dataset (69 long and 109 short sequences; see text for details). Posterior probability values ≥95% are shown. Species in blue reflect sequences that are 1050 bp in length, whereas those in black correspond to the 300 bp sequences. Grey branches indicate sequences with >98% homology in their respective genomes. For species lacking whole genome sequencing projects, that is manatee, hyrax, golden mole, sloth, bat, among others, yellow is used to indicate pairs of sequences with >98% homology. This yields a minimum estimate of the number of copies of potentially recently active L1 in these species. A species key shows the abbreviated names, scientific names and common names. The tree is broken into two sections. The inset shows which part of the tree is displayed.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1764860&req=5

pone-0000158-g001: Phylogenetic tree of LINE-1: combined dataset. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our concatenated dataset (69 long and 109 short sequences; see text for details). Posterior probability values ≥95% are shown. Species in blue reflect sequences that are 1050 bp in length, whereas those in black correspond to the 300 bp sequences. Grey branches indicate sequences with >98% homology in their respective genomes. For species lacking whole genome sequencing projects, that is manatee, hyrax, golden mole, sloth, bat, among others, yellow is used to indicate pairs of sequences with >98% homology. This yields a minimum estimate of the number of copies of potentially recently active L1 in these species. A species key shows the abbreviated names, scientific names and common names. The tree is broken into two sections. The inset shows which part of the tree is displayed.
Mentions: Since most LINE-1 copies are 5′-truncated and subsequently evolve as pseudogenes [1] they accumulate open reading frame (ORF) terminating, nonsense, and indel mutations. As expected, most of the 52 clones sequenced herein exhibit gaps and are non-active elements. Overall, five aardvark, three golden mole, one elephant and one bat clone displayed an ORF. It is probable that these represent a recent class of transposon not having had sufficient time to acquire mutations in this region. To further determine which lineages appeared recently active, all elements from the extended dataset were BLASTed against their genome of origin, and any that gave full-length hits with homologies higher than 98% have their branches coloured grey in Figure 1. A divergence of 2% is approximately 5 million years at the relatively slow rate that apes (e.g., chimp, human) evolve, or ∼1–3 million years for murid rodents which show the most rapid rates of change (along with tenrec) on our trees. These blast searches can of course be done only in those species for which there are at least whole genome shotgun sequence data (armadillo, elephant, tenrec, human, chimp, macaque, rabbit, mouse, rat, cow, dog). Therefore, to estimate recent activity in the absence of these data (for Cape serotine bat, aardvark, Cape golden mole, Cape elephant shrew, Cape rock hyrax, Cowan's shrew tenrec, Florida manatee, six-banded armadillo, tree anteater, pale-throated three-toed sloth), pairwise distances of closely related LINE-1 were checked, and any pair of sequences that were >98% similar to each other are coloured yellow in the tree (Figure 1). This gives a reasonable estimate of recently active LINE-1 in our dataset.

Bottom Line: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics.Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up.Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.

ABSTRACT

Background: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.

Methodology: To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.

Principal findings: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis.

Significance: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

Show MeSH
Related in: MedlinePlus