Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

Abstract

Background: Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available.

Results: We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies ( https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline ). Annotation results indicated a similar proportion of each genomes comprising TEs (35-36%). Class I LTR retrotransposons comprised 16-20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1-2% of each genome.

Conclusions: The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

Keywords: Camelid genomes; De novo TEs annotation; Retrotransposons; Transposable elements; Transposons.

Fig. 1

Flowchart for de novo identification of canonical TE sequences using both structural and homology-based approaches

Fig. 2

Genome assembly assessment and TE proportions. The BUSCO dataset of the mammalia_db9 including 4,104 BUSCO was utilized to evaluate the four camelid assemblies (A). TE proportions in the four camelid genomes (B)

Fig. 3

Distributions of LTR-RT ages in each of the four camelid genomes, with speciation event interval demarcated by vertical dashed lines. Phylogenetic relationships among species are depicted by the tree on the right

Fig. 4

LTR-RT length distributions in the four camelid genomes

Fig. 5

Distributions of LTR-RT cluster sizes for clusters delineated using the 80-80-80 rule. The y-axis is log(10)-transformed. Small horizontal lines represent individual clusters; their lengths are proportional to the number of clusters with that particular size, with the exception of the line for cluster size = 2, which is shortened to save space. Thick horizontal lines are means and the dotted horizontal line is the overall mean. Singletons are included as counts at the bottom of the plot

Fig. 6

Phylogenetic tree for LTR-RTs in cluster 6 of the ERV1 group in Vicugna pacos, with diagrams showing LTR domain structure (A) and two exemplar elements from cluster 4 (B)

Fig. 7

Phylogenetic tree for LTR-RTs in cluster 2 of the ERVL group in V. pacos, with diagrams showing LTR domain structure