Incomplete concerted evolution of nrDNA ITS in Lycium / 药学学报

In this study, nrDNA ITS sequences of Lycium cultivars were sequenced and used to test the existence of incomplete concerted evolution and pseudogenes. Together with 44 ITS sequences retrieved from GenBank, the pattern of base substitutions, GC content, 5.8S conserved motifs, the minimum free energy of secondary structures, nucleotide diversity and phylogenetic relationship of the samples were analyzed. While 83 of the 144 sequences were identified as pseudogenes, the results suggested a high degree of polymorphism and putative pseudogenes in Lycium, suggesting an incomplete concerted evolution of the ITS region. ITS polymorphism and pseudogene of Lycium were systematically tested for the first time. This research provides a references for ITS sequence to be used in the study of Lycium germplasm resources and DNA barcode identification.

Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange

ABSTRACT In Colombia Aedes aegypti is present in 80% of the country up to 2,300 m; however, little is known of its genetic relations within a country context and, hence, within a broader context, for example, America. The aforementioned, herein, analyzed the gene flow within a context of the Americas, its directionality and genetic diversity of the mitochondrial lineages in the A. aegypti populations for Colombia. This called for the use of the sequences for A. aegypti available of the mitochondrial ND4 gene in the GenBank for Colombia and the American continent. No presence was found of nuclear mitochondrial pseudogenes (NUMTs) for Colombia. It is estimated that in Colombia the gene flow of the A. aegypti populations is occurring from the southeast and northeast toward the center of the country. In comparison with the mitochondrial sequences for America, the vector's haplotypes in Colombia suggest connections between the populations of mosquitoes from the south with those from the north of the continent. The gene flow model at continental scale suggests bidirectional connections between the populations from the north of the continent with those from the south, while at South American scale it proposes the gene flow in all the directions with respect to the Colombian. The Colombian A. aegypti vector monitoring and control strategies must pay special attention to the vector's points of entry into Colombia related with Peru, Venezuela, Brazil, Mexico, and North America to avoid the entry of populations with characteristics like resistance to insecticides or vector competition.

sideRETRO: uma ferramenta de bioinformática dedicada à identificação deinserções polimórficas, germinativas ou somáticas, de pseudogenes processados / sideRETRO: a bioinformatics tool for identifying somatic and polymorphic insertions of processed pseudogenes

Os avanços metodológicos e instrumentais decorrentes do Projeto Genoma Humano formaram o arcabouço necessário para o surgimento das tecnologias de sequenciamento de DNA de Nova Geração, as quais se caracterizam por um custo reduzido, uma baixa demanda operacional e a produção de um grande volume de dados por experimento. Concomitantemente a isso, o aumento no poder de processamento computacional permitiu o desenvolvimento de análises genéticas em larga escala, de modo que, atualmente, é possível estudar características genômicas individualizadas e, até então, pouco ou nunca exploradas. Dentre essas características, aquelas relacionadas às variações estruturais em genomas têm recebido bastante atenção. Os pseudogenes processados, ou retrocópias, são variações estruturais causadas pela duplicação de genes codificadores mediante à transposição de seu RNA mensageiro maduro pela maquinaria enzimática de LINE- 1. As retrocópias podem estar fixadas, ou seja, presentes em todos os genomas de uma dada espécie, os quais são representados pela montagem modelo do genoma de referência, ou podem não estar fixadas, sendo polimórficas, germinativas ou somáticas. No entanto, o conhecimento acerca das retrocópias não fixadas ainda é limitado devido à falta de ferramentas de bioinformática dedicadas a sua identificação e anotação em dados de sequenciamento de DNA. Posto isso, este trabalho apresenta o sideRETRO um programa computacional especializado na detecção de pseudogenes processados ausentes do genoma de referência, mas presentes em dados de sequenciamento de genoma completo e exoma de outros indivíduos. Além de apontar para a presença de retrocópias não fixadas, o sideRETRO é capaz de anotar várias outras características relacionadas a esses evento, tais como: a coordenada genômica de inserção do pseudogene processado, a qual constitui o cromossomo, o ponto de inserção e a fita de DNA (líder or retardada); o contexto genômico do evento (exônico, intrônico ou intergênico); a genotipagem (presente ou ausente) e a haplotipagem (em homozigose ou heterozigose). Para atestar a eficiência da ferramenta, o sideRETRO foi executado para dados simulados e para dados reais validados experimentalmente por um grupo independente. Portanto, em resumo, nesta tese são descritos o desenvolvimento e o uso do sideRETRO uma ferramenta computacional robusta e eficiente, designada para identificar e anotar pseudogenes processados não fixados. Por fim, vale destacar que o sideRETRO preenche uma lacuna metodológica e possibilita novas hipóteses e investigações sistemáticas no campo de chamada de variantes estruturais

The methodological and instrumental advances resulting from the Human Genome Project have created the necessary framework to the emergence of Next Generation DNA sequencing technologies, which are characterized by a reduced cost, low operational demand and the generation of a large volume of data per experiment. Concomitantly with this, the increase in computational processing power has driven the development of large-scale genetic analyses, which allowed us to study individualized genomic traits little or never explored before. Among these characteristics, those related to structural variations in genomes have received much attention. Processed pseudogenes, or retrocopies, are structural variations caused by the duplication of coding genes through the transposition of their mature messenger RNA by the LINE-1 enzymatic machinery. Retrocopies can be fixed (i.e., present in all genomes of a given species and included into the assembly of the reference genome) or unfixed, being polymorphic, germinal or somatic. However, knowledge about unfixed retrocopies is still limited due to the lack of bioinformatics tools dedicated to their identification and annotation in DNA sequencing data. Therefore, this work presents sideRETRO a computer program specialized in the detection of processed pseudogenes absent from the reference genome, but present in whole genome and exome sequencing data from other individuals. In addition to pointing out the presence of unfixed retrocopies, sideRETRO is able to annotate several other characteristics related to these events, such as: the genomic coordinate of the processed pseudogene insetion, which constitutes the chromosome, the insertion point and the DNA strand (leader or retard); the genomic context of the event (exonic, intronic or intergenic); genotyping (present or absent) and haplotyping (homozygous or heterozygous). To certify the sideRETRO efficiency, it was run on simulated data and on real data experimentally validated by an independent group. Therefore, in summary, this thesis describes the development and use of sideRETRO a robust and efficient computational tool, designed to identify and annotate unfixed processed pseudogenes. Finally, it is worth noting that sideRETRO fills a methodological gap and allows new hypotheses and systematic investigations in the field of structural variant calling

Research progress in the competing endogenous RNA in gastric cancer pathogenesis / 中华检验医学杂志

Recent studies demonstrate that the long non-coding RNAs (lncRNAs), pseudogenes, circular RNAs (circRNAs) and so on can be used as competitive endogenous RNAs (ceRNAs), binding to microRNAs (miRNAs), to regulate the expression level of their targets.This novel interplay optimizes traditional liner miRNA→RNA pattern and has become a research hotspot in the scientific community.Dysregulation of ceRNA interplay will influence the body′s normal life activities, leading to the occurrence of diseases, and even tumor formation.This article briefly introduces the key components of ceRNA crosstalk and its research progress in gastric cancer pathogenesis, so as to provide a new thought for cancer research, clinical diagnosis and therapeutics.

Mecanismos de Variación Antigénica en Anaplasma marginale / Mechanisms of Antigenic Variation in Anaplasma marginale

Anaplasma marginale (A. marginale), es una bacteria del orden de las Rickettsias que ocasiona la anaplasmosis bovina en regiones tropicales y subtropicales del mundo. Esta enfermedad, trasmitida principalmente por tábanos y garrapatas, se desarrolla típicamente en una etapa inicial aguda con manifestaciones clínicas caracterizadas principalmente por anemia y fiebre. Después de un par de meses, los animales recuperan su condición física y se hacen asintomáticos, siendo incapaces de eliminar completamente la bacteria, convirtiéndose en animales persistentemente infectados. Esto se debe a la capacidad de A. marginale para evadir el sistema inmune. En este sentido, se ha demostrado la existencia de un mecanismo de variación antigénica en las proteínas MSP1, MSP2 y MSP3 de la bacteria. Al evaluar la familia multigénica que codifica para la MSP2, se determinó que está conformada por dos regiones conservadas que flanquean una región central hipervariable. De esta manera, al expresarse cada una de las 52 variables de la MSP2, se expresa un epítope diferente. Cuando se describió el genoma completo de este hemotrópico, se encontró también la presencia de 16 pseudogenes msp2, los cuales pueden ser recombinados dentro del sitio de expresión del operón de la MSP2, constituyendo un segundo mecanismo de variación. Además de ello, los fragmentos hipervaribles y los pseudogenes se pueden combinar entre sí, en un proceso denominado conversión génica, creando nuevos epítopes “recombinantes”, confiriendo una capacidad de variabilidad antigénica casi infinita al A. marginale (tercer mecanismo). Un cuarto mecanismo de variación antigénica, lo constituye la dimerización de la MSP2 sobre la superficie del A. marginale, debido a que la expresión simultánea de variantes conforman epítopes únicos. En conclusión, la recombinación génica de la MSP2 y su dimerización en la membrana, constituye un mecanismo muy eficiente de variación antigénica para eludir el sistema inmunológico del hospedador.

Anaplasma marginale (A. marginale) is a bacterium of the Rickettsiales order that causes bovine anaplasmosis in tropical and subtropical regions worldwide. This disease, mainly transmitted by ticks and horseflies, typically develops in an initial acute stage, with clinical signs characterized by anemia and fever. After two months, animals recover their original physical condition and become asymptomatic, being unable to completely eliminate the bacterium, turning into persistently infected animals. This is due to the ability of A.marginale to evade the immune system. In this regard, the existence of a mechanism for antigenic variation in proteins of the bacterium, such as MSP1, MSP2, and MSP3, has been demonstrated. When assessing the multigenic family which encodes for MSP2, it was determined that it consists of two conserved regions flanking a central hypervariable region. Thus, when expressing each of the 52 MSP2 variables, a different epitope is also expressed. When the entire genome of this parasite was decoded, the presence of 16 pseudogenes for MSP2 was also discovered. These pseudogenes can be recombined within the operon expression site of MSP2, providing a second mechanism of variation. Moreover, both the hypervariable fragments and pseudogenes can combine among them, in a process called gene conversion, creating new “recombinant” epitopes, conferring the A. marginale with an almost infinite capacity for antigenic variability (third mechanism). A fourth mechanism of antigentic variation consists of the dimerization of MSP2 on the surface of A. marginale, because the simultaneous expression of variants creates unique epitopes. In conclusion, gene recombination of MSP2 along with the dimerization of MSP2 on the membrane provides a very efficient mechanism for antigenic variation for evading the host’s immune system.

Characterization of pseudogenes in members of the order Frankineae.

Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.

A new method avoids interference of ABCD1 pseudogenes in molecular diagnosis of X-linked adrenoleukodystrophy / 第二军医大学学报

Objective: To introduce a new method which can avoid the interference of ABCD1 pseudogenes in the molecular diagnosis of X-linked adrenoleukodystrophy. Methods: The coding regions of ABCD1 gene of 3 unrelated Chinese patients with X-linked adrenoleukodystrophy were amplified from the total RNA of peripheral blood by long distance RT-PCR; the product was further amplified in 4 segments in a second round PCR; and the PCR products were purified and directly sequenced. To confirm the mutations, the genomic DNA from peripheral blood cells of the patients was analyzed by direct sequencing after amplification of the ABCD1 genes by nested PCR, in which the product of the first round PCR covered the fragment starting from exon 6 and ending at 3′UTR of the ABCD1 gene. Results: The 3 Chinese patients with X-linked adrenoleukodystrophy had 3 different base substitutions(2235C>T,2065C>T and 2190A>T)in the ABCD1 genes of the 3 probands and their mothers, which resulted in 2 missense mutations (R617C and P560L) and one nonsense mutation (K602X). Conclusion: Nested PCR can rapidly and efficiently avoid the interference of ABCD1 pseudogenes in the molecular diagnosis of X-ALD.

High Correlation between Alu Elements and the Conversion of 3' UTR of mRNAs Processed Pseudogenes

Even though it represents 6 13% of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over 80 % of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about 10% of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.