El genero Neotropical Pseudopimelodus es el segundo con la mas amplia distribucion de la familia Pseudopimelodidae en Sur America y comprende cuatro especies validas que habitan en diferentes rios trans y cis-andinos. De estas cuatro especies, dos se encuentran registradas en Colombia: P. schultzi distribuida en las cuencas Magdalena-Cauca y Caribe y P. bufonius en el rio Atrato y en las cuencas Amazonas y Orinoco. Diversos procesos paleogeograficos resultantes de la orogenia Andina en Suramerica noroccidental podrian promover la diversificacion genetica del genero Pseudopimelodus en Colombia. Para contrastar esta hipotesis, en este trabajo se realizaron analisis filogeneticos basados en Inferencia Bayesiana usando secuencias parciales del gen nuclear activador de la recombinacion (rag2) y de la subunidad 1 del gen de la Citocromo C Oxidasa (COI). Adicionalmente, se realizo la descripcion de dos nuevas especies de Pseudopimelodus para la cuenca Magdalena-Cauca mediante el analisis de caracteres osteologicos y morfometricos: Pseudopimelodus sp. nov. 1 presente en la parte media y alta del Rio Cauca y parte alta del Rio Magdalena y Pseudopimelodus sp. nov. 2 que habita en la parte baja del Rio Cauca y parte media y baja del Rio Magdalena. Por otro lado, este estudio desarrollo un conjunto de 13 microsatelites utilizando tecnologia de secuenciacion de proxima generacion para evaluar la diversidad y la estructura genetica de estas dos nuevas especies de Pseudopimelodus. Los resultados obtenidos mediante Inferencia Bayesiana mostraron que el genero Pseudopimelodus en Colombia representan al menos cinco linajes evolutivos bien delimitados, cuyos tiempos de divergencia concuerdan con la historia geologica de Suramerica noroccidental. Ademas, los analisis obtenidos de los microsatelites mostraron que ambas especies exhiben altos niveles de flujo genetico entre los sitios muestreados y alta diversidad genetica en comparacion con los niveles promedios de diversidad genetica reportados para Siluriformes Neotropicales. Los resultados obtenidos en el presente trabajo son de suma importancia para el diseno e implementacion de estrategias regionales de manejo de las pesquerias de Pseudopimelodus en Colombia

Bumblebee catfishes in Colombia: disentangling macro and microevolution in the genus Pseudopimelodus (Siluriformes: Pseudopimelodidae)

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.

/pdf/accurate-typing-of-short-tandem-repeats-from-genome-wide-5ggkrfocgt.pdf

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Conservation initiatives are now more crucial than ever—over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.

https://www.mdpi.com/2073-4425/10/11/846/pdf

The Value of Reference Genomes in the Conservation of Threatened Species.

Background 
The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction.


Results 
The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats.


Conclusions 
This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.

/pdf/sequencing-de-novo-assembly-and-annotation-of-the-4pd3slav84.pdf

Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 –to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.

/pdf/microsatellites-in-pursuit-of-microbial-genome-evolution-59l1e0hc5q.pdf

Microsatellites in Pursuit of Microbial Genome Evolution

Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.

/pdf/application-of-microsatellite-markers-in-conservation-2w66q29w4f.pdf

Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.

P. M. Abdul-Muneer

Papers

Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.