Genes Devoid of Full-Length Transposable Element Insertions are Involved in Development and in the Regulation of Transcription in Human and Closely Related Species

2010 ◽  
Vol 71 (3) ◽  
pp. 180-191 ◽  
Author(s):  
Hussein Mortada ◽  
Cristina Vieira ◽  
Emmanuelle Lerat
Keyword(s):  
Transposable Element ◽  
Related Species ◽  
Full Length ◽  
Regulation Of Transcription ◽  
Closely Related Species

scholarly journals Evolutionary insights into Mariner-like elements in Apis species

2020 ◽  
Author(s):  
Kakeru Yokoi ◽  
Kiyoshi Kimura ◽  
Hidemasa Bono
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Element ◽  
Related Species ◽  
Horizontal Transfer ◽  
The Other ◽  
Closely Related Species ◽  
Sequences Analysis ◽  
Almost All

AbstractBackgroundMariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse. In previous reports, a few transposable element in the genomes of Apis species mainly consist of mariner and MLE. For further insight of Apis MLEs, detailed classifications of Apis MLE and sequences analysis of long MLEs, which may potentially encode the transposase, are needed.ResultsMuch more MLEs were detected in A. mellifera genome compared to other Apis species genomes. They were classified into 31 Drosophila MLE classes. In this classification, almost all of MLEs were classified into the three classes belonging to mellifera subfamilies, suggesting that Apis MLEs which exist thorough Apis species derived from single MLE belonging to mellifera subfamily. Phylogenetic analysis using MLEs in the three classes showed that there two types of clusters, of which one consist of multiple Apis species MLEs, and others of only A. mellifera MLEs. Long MLEs analysis showed that only one long MLE encoding complete transposase was found in all Apis genome except for A. mellifera genome, and the MLE and multiple MLEs similar to it were found in A. mellifera genome. The analysis also showed that other several long MLEs encoding complete transposase were found only in A. mellifera genome.ConclusionsAlmost all of Apis MLEs are mellifera subfamilies. Of these MLEs, one types of them settled in Apis species and burst in A. mellifera genome. The other one of MLEs invaded into A. mellifera genome by horizontal transfer and exploded in A. mellifera genome. This is the first example of the finer aspects of MLE evolution among closely related species.

scholarly journals Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

2020 ◽  
Author(s):  
Yinjie Qiu ◽  
Ya Yang ◽  
Cory D. Hirsch ◽  
Eric Watkins
Keyword(s):  
Illumina Sequencing ◽  
Related Species ◽  
Gene Discovery ◽  
Full Length ◽  
Cool Season ◽  
Illumina Platform ◽  
Closely Related Species ◽  
Reference Transcriptome ◽  
Low Input ◽  
Breeding And Genetics

Abstract Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and seed head tissues. We obtained 59,510 full-length transcripts, of which 38,595 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. To test the polyploid origin of F. brevipila, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the allopolyploid origin of F. brevipila. Conclusions: Overall, the F. brevipila Pacbio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders for gene discovery in this important turfgrass species.

scholarly journals Bursts of recent transposable element activity and signatures of element removal in the monarch genome, Danaus plexippus

2021 ◽  
Author(s):  
Tobias Baril ◽  
Alexander Hayward
Keyword(s):  
Transposable Element ◽  
Genome Assembly ◽  
Related Species ◽  
Draft Genome ◽  
Danaus Plexippus ◽  
Closely Related Species ◽  
Immune Genes ◽  
Genomic Deletions ◽  
The Impact ◽  
Element Removal

AbstractBackgroundLepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly of the monarch butterfly (Danaus plexippus), famous for its North American migration, is available but lacks an in-depth transposable element (TE) annotation. This provides an opportunity to explore host-TE interactions, and the impact TEs have in shaping the monarch genome.Results6.47% of the monarch genome is comprised of TEs, a reduction of 6.59% compared to the original TE annotation performed on the draft genome assembly. TE content is low compared to two closely related species, Danaus chrysippus (26.70%) and Danaus melanippus (11.87%). The biggest contributors to genome size in the monarch are LINEs and Penelope-like elements, and 37.7% of TE content is contributed by five newly identified TE families (two LINE, two Penelope-like, and one SINE). Some young DNA TE families show similar activity profiles to these LINEs, with their success putatively due to horizontal transposon transfer from species sharing the same environment. There are several recent peaks of TE activity in the monarch, with little evidence for peaks of activity more anciently. LINE fragments demonstrate signatures of genomic deletions as reported by studies on Heliconius butterflies, indicating a high rate of TE turnover. Given previous associations in other species, we investigated the association of TEs with wing colouration and immune genes. We find a single unclassified element 7kb upstream of the myosin gene locus, associated with wing colouration, and 49 immune genes with TEs within 5kb upstream of the transcription start site, presenting the potential for the involvement of TEs in regulatory functions.ConclusionsWe provide an in-depth TE annotation and analysis of TE diversity and evolution for the monarch genome. We identify highly successful novel DNA TE families, mirroring the activity profile of the most successful LINEs. We also find evidence of ongoing TE expansion and removal in the monarch, highlighting the dynamic nature of repeat content in genomes over time. Further in-depth comparative studies across closely related species will be beneficial to our understanding of the evolutionary dynamics of TEs and the processes leading to their contrasting distributions.

Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)

2020 ◽  
Vol 9 (3) ◽  
pp. 160-170
Author(s):  
Thumadath P.A. Krishna ◽  
Maharajan Theivanayagam ◽  
Gurusunathan V. Roch ◽  
Veeramuthu Duraipandiyan ◽  
Savarimuthu Ignacimuthu
Keyword(s):  
Molecular Marker ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Related Species ◽  
Finger Millet ◽  
Crop Improvement ◽  
Human Beings ◽  
Closely Related Species ◽  
Genome Amplification

Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

Sign in / Sign up

Export Citation Format

Share Document