Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
Fluorescence in situ hybridization (FISH) analysis has shown previously that 10-15% of chronic myeloid leukemias (CML) have hemizygous deletions of variable sizes affecting regions that flank the ABL and BCR translocation breakpoints on the derivative chromosome 9, and these patients have a poor outcome. FISH studies using large commercial genomic probes have previously suggested that haploinsufficiency of sequences flanking either ABL or BCR modify the disease process of CML and lead to an unfavorable prognosis. In this present study, real-time quantitative PCR (Q-PCR) analysis was used to identify and map much smaller hemizygous microdeletions in a subset of CML patients that were not deleted using large genomic FISH probes. Microdeletions were identified by Q-PCR in 25 of 71 patients selected based on less favorable outcome (chronic phase duration of less than 96 months and a survival time of less than 84 months). In contrast, no microdeletion was detected in any of 18 CML samples selected from a group with a more favorable outcome. Detailed mapping of the 25 Q-PCR microdeletions showed that the minimal deleted region extended approximately 120 kb from the 5' end of the ABL gene in the centromeric direction on the derivative chromosome 9, and the region 3' to BCR on chromosome 22 was excluded. Of the four ESTs and/or genes that map to the 120 kb region, the putative tumor suppressor PRDM12 is the strongest candidate gene. The potential role for each sequence in modifying the clinical behavior of CML is presented.
The Cyprinidae is the largest freshwater fish family in Vietnam, with over 220 recognised species, many of which play an important role in aquaculture or are harvested from the wild. Despite numerous studies on the taxonomy of this family based on traditional morphological data, the relationships between major cyprinid groups is poorly understood and the taxonomic validity of a number of these groups is under debate. While an increasing number of molecular studies on cyprinid relationships have been conducted many have used restricted sampling and none have incorporated Vietnamese species. In this study, mitochondrial 16S rRNA, D-loop and cytochrome b gene sequences from 25 species of cyprinids collected from Vietnam were obtained and combined with sequences of cyprinids available in GenBank, in order to investigate the taxonomic validity of subfamilies within Cyprinidae and their phylogenetic relationships. The molecular data supported traditional division of the Cyprinidae into two major lineages: Cyprinines and Leuciscines. The placement of the Danioninae as the sister lineage to this grouping was not supported. Many of the subfamily boundaries were questioned and doubt was raised on some of the generic level classifications. The validity of species designation in Cyprinus, Tor and Cyclocheilichthys was also questioned. This study will need to be extended with greater taxon and gene sampling to further consolidate our understanding of cyprinid relationships and classification.Résumé -Evaluation phylogénétique de la classification en sous-familles des Cyprinidae, en considérant les espèces du Vietnam en particulier. La plus grande famille de poissons d'eau douce, au Vietnam, est celle des Cyprinidae, avec plus de 220 espèces identifiées ; la plupart de ces espèces joue un rôle important en aquaculture ou bien sont pêchées. Bien que de nombreuses études sur la taxonomie de cette famille soient basées sur des données morphologiques traditionnelles, les relations entre les grands groupes de Cyprinidae sont peu connues, et la validité taxonomique de ces groupes reste à discuter. Pourtant, un nombre croissant d'études moléculaires sur les relations entre les groupes de Cyprinidae ont été conduites, mais souvent sur des échantillonnages réduits, et aucune n'a tenu compte des espèces du Vietnam. Dans cette étude, les gènes mitochondriaux codant pour l'ARNr 16S, D-loop (la région de contrôle) et le cytochrome b de 25 espèces de Cyprinidae collectés au Vietnam ont été obtenus et combinés avec ceux des Cyprinidae disponibles dans « GenBank », en vue d'analyser la validité taxonomique des sous-familles de Cyprinidae et leurs relations phylogénétiques. Les données moléculaires s'appuient sur la division traditionnelle des Cyprinidae en deux grandes lignées : Cyprininae et Leuciscinae. La place des Danioninae en tant que lignée soeur n'est pas soutenue. Les frontières entre de nombreuses sous-familles sont floues, et soulèvent quelques doutes sur le niveau de classification au niveau des genres. La validité des espèces dési...
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