Retrotransposons

SUMMARY Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in Brassica napus (A n A n C n C n) with the Brassica rapa (A r A r) genome by two rounds of interspecific hybridization resulted in a new introgressed type of B. napus (A r A r C n C n). In this study, we construct a population of recombinant inbred lines of the new introgressed type of B. napus. Microsatellite, intron-based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield-related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield-related traits in the introgressed B. napus to an even greater extent than the alleles alone that were introgressed from the A r subgenome of B. rapa, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.

Arthropods
ISSN 2224-4255

Volume 8, Number 1, 1 March 2019

Cover Pages

[Front Pages (332K)] [Back Pages (55K)]
Articles

Early developmental stage of Pentapycnon charcoti Bouvier
Arthropods, 2019, 8(1): 1-6
John A. Fornshell, Austin Patrick Harlow
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Characterization of two non-LTR retrotransposons from Sogatella furcifera and Nilaparvata lugens
Arthropods, 2019, 8(1): 7-16
Jia Lin, Mei Zhang, JingYi He, GuangHong Li, FangHai Wang
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Describing selected populations of the rice black bugs in the Philippines using Correlation Analysis Based on Distances (CORIANDIS)
Arthropods, 2019, 8(1): 17-31
Melbert C. Sepe, Mark Anthony J. Torres, Ravindra C. Joshi, Cesar G. Demayo
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Effect of different temperatures on food consumption of juveniles shrimp Metapenaeus affinis (H. Milne Edwards, 1837)
Arthropods, 2019, 8(1): 32-37
Tariq H. Y. Al-Maliky, Sajed S. Al- Noor, Malik H. Ali
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A review on studies of behavioural ecology of Centrobolus (Diplopoda, Spirobolida, Pachybolidae) in southern Africa
Arthropods, 2019, 8(1): 38-44
Mark Cooper
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In vitro clonal propagation of plants should generate identical copies of the selected genotype. However, associated stress might result in a breakdown of control mechanisms and consequent instability of the genome. We have used several molecular methods to assess the genetic stability of long-term propagated (24 years) multiple shoot in vitro culture of pea (Pisum sativum L.). We focused on assessing the stability of repetitive sequences, such as simple sequence repeats (SSR) and retrotransposons, both comprising a large part of genome. No differences were found when seedlings (Co-2004) or original seed (Co-1982) controls and long-term or newly established in vitro (one subculture cycle) samples were investigated by the SSR, inter-repeats (ISSR) or inter-retrotransposon amplified polymorphism (IRAP) method. However, the more global amplified fragment length polymorphism (AFLP) and particularly the methylation sensitive MSAP methods detected 11 and 18% polymorphism among samples, respectively. Interestingly, investigation of the global cytosine methylation status by HPCE measurement revealed no statistically significant differences. Some evidence of retrotransposon re-arrangement was observed by sequence-specific amplification polymorphism. This occurred mostly in the abundant Ty3-gypsy type Cyclop element and to a smaller extent in the Ogre element. Alternatively, no polymorphism was detected among the PDR-1 element of the Ty1-copia type retrotransposon. Based on these results, multiple shoot culture of pea maintained over a long period may be considered as a true to type multiplication method of the original genotype.

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.

In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. 

Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Available from: https://www.researchgate.net/publication/317165661_Canine_Brachycephaly_Is_Associated_with_a_Retrotransposon-Mediated_Missplicing_of_SMOC2 [accessed May 29, 2017].

The long 5'-untranslated region (5'-UTR) of the human L1 retrotransposon contains a unique internal promoter, allowing new L1 copies to be less dependent on the integration site at the transcriptional level. The mechanism of action of this promoter still remains unclear; however, some early studies have build up an opinion that the first 5'-UTR segment of 100–150 nt (known as the minimal promoter) is most crucial for the functioning of the full-length promoter. This study shows that the activity of the minimal promoter is rather low in comparison with the activity of the full-length 5'-UTR. Instead, 5'-UTR internal segment 390–662, containing numerous binding sites for various transcription factors, is indispensable for effective L1 transcription and can be considered as a transcriptional enhancer. Deletion of this segment dramatically reduces the level of transcription irrespective of the cell type, whereas deletion of the first 100 nt decreases the transcription level only by a factor of 1.5–2. Thus, the L1 regulatory region remains to be structurally similar to that of well-studied invertebrate LINEs. It is also possible that the internal 5'-UTR segment of L1 contains an alternative promoter, driving synthesis of a 5'-truncated L1 mRNA.

La linea BLS1A posee un sistema de letales balanceados localizado en las cercanias del centromero del cromosoma 6 de maiz formado por un gen letal clorofilico estrechamente ligado en fase de repulsion con un gen letal gametico. Los objetivos de esta tesis fueron los de caracterizar agronomica y molecularmente el segmento cromosomico balanceado de la linea de maiz BLS1A. Los resultados de ensayos a campo mostraron diferencias estadisticamente significativas entre BLS1A y algunos de sus recombinantes. La linea BLS1A mantuvo su vigor a pesar de los anos de endocria. La caracterizacion genetica a nivel molecular se realizo a traves de la busqueda de polimorfismos con marcadores moleculares de RAPD, RFLP, STS, AFLP y Microsatelites. Se analizaron mas de 13200 loci genicos en todo el genoma de las lineas. Cinco microsatelites resultaron polimorficos para en el segmento y se lograron clonar y secuenciar siete bandas de RAPD y AFLP que mapearon en la region cromosomica en estudio. Las tecni...

Recent progress in sequencing the genomes of several Leishmania species, causative agents of cutaneous, mucocutaneous and visceral leishmaniasis, is revealing unusual features of potential relevance to parasite virulence and pathogenesis in the host. While the genomes of Leishmania major, Leishmania braziliensis and Leishmania infantum are highly similar in content and organisation, species-specific genes and mechanisms distinguish one from another. In particular, the presence of retrotransposons and the components of a putative RNA interference machinery in L. braziliensis suggest the potential for both greater diversity and more tractable experimentation in this Leishmania Viannia species.

Recent progress in sequencing the genomes of several Leishmania species, causative agents of cutaneous, mucocutaneous and visceral leishmaniasis, is revealing unusual features of potential relevance to parasite virulence and pathogenesis in the host. While the genomes of Leishmania major, Leishmania braziliensis and Leishmania infantum are highly similar in content and organisation, species-specific genes and mechanisms distinguish one from another. In particular, the presence of retrotransposons and the components of a putative RNA interference machinery in L. braziliensis suggest the potential for both greater diversity and more tractable experimentation in this Leishmania Viannia species.

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Keywords: Human transposable element LINE1 Retrotransposon L1 5′ UTR Promoter activity Transcription start site mapping Transcriptional enhancer L1 (LINE-1) is one of the most abundant families of human transposable elements. Full-length human L1 has an ~ 900 bp long 5′ untranslated region (5′ UTR) which harbors an internal promoter for the RNA polymerase II. It is generally accepted that the first 100 bp of the 5′ UTR function as a " minimal promoter " which directs transcription of the entire LINE-1 unit from the extreme 5′ terminus. We re-investigated promoter activities of the different DNA fragments that cover the whole L1 5′ UTR in cultured human cells by using the luciferase reporter system. Analysis of both mRNA expression and luciferase activity levels indicated that the very important region for the effective transcription is located within the internal part of the L1 5′ UTR between nucleotide positions +390 and + 526. 5′ RACE analysis revealed that in the context of the complete 5′ UTR, this part drives mRNA synthesis both from the canonical 5′-terminal transcription start site (TSS) and from within the internal region. In the absence of the first 100 bp, the L1 5′ UTR efficiently directed transcription from aberrant TSSs located within its 3′ proximal part or the ORF1. Finally, we analyzed transcripts originated from endogenous (genomic) L1 elements and identified two novel TSSs located at positions + 525 and + 570. We propose a model in which the internal part (390–526) of the L1 5′ UTR plays a key role for recruitment of transcription initiation complex, which then may be either positioned onto the 5′ terminally located " minimal promoter " , or used proximately to direct 5′ truncated RNA copy. Intriguingly, this internal regulatory element substantially overlaps with the region of the L1 5′ UTR that is known to drive transcription in the opposite direction suggesting the existence of a common core for the bidirectional transcription.