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.

LTR Retroelements and Bird Adaptation to Arid Environments

“…Indeed, these lineages underwent a radiation about 30 Mya when Earth’s climate was destabilized by dramatic changes, and Australia started to experience progressive aridification across most of its landmasses. The bird LTR retroelement expansion might have represented an evolutionary advantage in the adaptation to arid/drought environments, in line with that reported in other species [ 40 , 41 , 42 , 43 ]. It is known that LTR retroelements can control the transcription of host gene by inserting cis-regulatory sequences such as enhancers, promoters, and insulators [ 57 , 58 ].…”

“…This observation is also supported by variation partitioning analysis, which revealed a better correlation between LTR retroelement content and climate changes that occurred in Australia and Antarctica during the Eocene-Oligocene transition than the phylogeny of the species analyzed. In plants, LTR retroelements have been reported to be activated under drought stress conditions [ 40 , 41 , 42 ], and in animals, a prevalence of these TE elements has been identified in the genome of the genus Camelus adapted to arid environments [ 43 ]. In support of our hypothesis, Australian species living in temperate and tropical regions, such as P. strigoides , A. lathami , and P. torquatus ( Figure 7 ), showed a limited fraction of LTR retroelements and a strong prevalence of LINE retroelements, as reported also for the C. casuarius genome.…”

Comparative genomics reveals insights into anuran genome size evolution

“…Genome-wide data versions, release dates and database information are available in the supplementary material (Supplementary Materials 1: Table S1 ). To ensure the accuracy of our datasets, following the methods of Ibrahim et al [ 75 ], we collected the information on the genome completeness data of 14 anuran species from the NCBI and relevant citations (referring to Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results [ 76 ]). This data includes information such as the number of scaffolds, scaffold N50, contigs, contig N50, genome assembly level, and genome size (referring to the assembly size) (Supplementary Materials 1: Table S1 ).…”

High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes

“…Comparative analyses of LTR element distribution aid in deciphering underlying factors influencing their evolutionary dynamics, and investigating the effect of LTR element domestication uncovers novel genetic elements and regulatory mechanisms [40][41][42]. In the present study, we investigated the abundance and variety of LTR-RTN families in ten concentrated tetraodontiform genomes, revealing intriguing patterns and insights into LTR distribution dynamics.…”