Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus.
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ABSTRACT:
SUBMITTER: Ouyang Z
PROVIDER: S-EPMC8146837 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundGenome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels.ResultsAfter determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species.ConclusionsThis large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species.
| S-EPMC5563062 | biostudies-literature
Project description:Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5-5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation.
| S-EPMC4718150 | biostudies-literature
Project description:SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined.
| S-EPMC4163409 | biostudies-literature
Project description:Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.
| S-EPMC6010443 | biostudies-literature
Project description:BackgroundLong Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences.ResultsIn this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established.ConclusionsThe data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.
| S-EPMC8127270 | biostudies-literature
Project description:In vertebrates, DNA methylation-mediated repression of retrotransposons is essential for the maintenance of genomic integrity. In the current study, we developed a technique termed HT-TREBS (High-Throughput Targeted Repeat Element Bisulfite Sequencing). This technique is designed to measure the DNA methylation levels of individual loci of any repeat families with next-generation sequencing approaches. To test the feasibility of HT-TREBS, we analyzed the DNA methylation levels of the IAP LTR family using a set of 12 different genomic DNA isolated from the brain, liver and kidney of 4 one-week-old littermates of the mouse strain C57BL/6N. This technique has successfully generated the CpG methylation data of 5,233 loci common in all the samples, representing more than 80% of the individual loci of the five targeted subtypes of the IAP LTR family. According to the results, approximately 5% of the IAP LTR loci have less than 80% CpG methylation levels with no genomic position preference. Further analyses of the IAP LTR loci also revealed the presence of extensive DNA methylation variations between different tissues and individuals. Overall, these data demonstrate the efficiency and robustness of the new technique, HT-TREBS, and also provide new insights regarding the genome-wide DNA methylation patterns of the IAP LTR repeat elements.
| S-EPMC4086960 | biostudies-literature
Project description:Centromere-binding protein B (CENP-B) is a widely conserved DNA binding factor associated with heterochromatin and centromeric satellite repeats. In fission yeast, CENP-B homologues have been shown to silence long terminal repeat (LTR) retrotransposons by recruiting histone deacetylases. However, CENP-B factors also have unexplained roles in DNA replication. Here we show that a molecular function of CENP-B is to promote replication-fork progression through the LTR. Mutants have increased genomic instability caused by replication-fork blockage that depends on the DNA binding factor switch-activating protein 1 (Sap1), which is directly recruited by the LTR. The loss of Sap1-dependent barrier activity allows the unhindered progression of the replication fork, but results in rearrangements deleterious to the retrotransposon. We conclude that retrotransposons influence replication polarity through recruitment of Sap1 and transposition near replication-fork blocks, whereas CENP-B counteracts this activity and promotes fork stability. Our results may account for the role of LTR in fragile sites, and for the association of CENP-B with pericentromeric heterochromatin and tandem satellite repeats.
| S-EPMC3057531 | biostudies-literature
Project description:Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
| S-EPMC4379980 | biostudies-literature
Project description:BackgroundLTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact.ResultsUsing LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor.ConclusionsUse of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size.
| S-EPMC5006616 | biostudies-literature
Project description:LTR retrotransposons are repetitive DNA elements comprising ?10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active ?-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells. We found that the ERV-9 LTR, containing 65 CpGs in 1.7 kb DNA, was hypermethylated (with > 90% methylated CpGs). Hypermethylated LTR possessed transcriptional enhancer activity, since in vivo deletion of the LTR by CRISPR-cas9 suppressed transcription of the globin genes by > 50%. ChIP-qPCR and ChIP-seq studies showed that the hypermethylated LTR enhancer spanning recurrent CCAATCG and GATA motifs associated respectively with key transcription factors (TFs) NF-Y and GATA-1 and -2 at reduced levels, compared with the unmethylated LTR in transfected LTR-reporter gene plasmids. Electrophoretic mobility shift assays with methylated LTR enhancer probe showed that the methylated probe bound both NF-Y and GATA-1 and -2 with lower affinities than the unmethylated enhancer probe. Thus, hypermethylation drastically reduced, but did not totally abolish, the binding affinities of the enhancer motifs to the key TFs to assemble the LTR-pol II transcription complex that activated transcription of cis-linked genes at reduced efficiency.
| S-EPMC5406212 | biostudies-literature