Comparative Analysis of Ribosomal Protein Gene, eL14 Expression between Two Types of Colorectal Carcinoma Cell Lines

Association between the expression of ribosomal protein (RP) genes and cancer is widely known. More specifically, the extra-ribosomal functions of RPs have been linked to carcinogenesis. The ribosomal protein gene, eL14 has been reported to be associated with malignancy of the colorectum, albeit of mechanism yet unclear. Its expression in cells derived from different tissue origin of colorectal carcinoma (CRC) has never been explored. Therefore, this study aims to comparatively analyse the expression pattern of eL14 between two different CRC cell lines (DLD-1 and HCT116). It involved a conventional gene expression analysis, the Reverse-Transcriptase PCR (RT-PCR) assays. Products of RT-PCR assay were resolved via an agarose gel electrophoresis method, and band intensities of amplicons were documented and quantified using TotalLab Quant software. We observed differential expression patterns of eL14 between DLD-1 and HCT116 cells, but statistical analysis revealed insignificant differences. Therefore, the relevance of eL14 as a biomarker to distinguish between different colorectal cancer cells is suggestive but not conclusive

The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra)

The Javan mahseer ( Tor tambra ) is one of the most valu- able freshwater fish found in Tor species. To date, other than mitogenomic data (BioProject: PRJNA422829), genomic and transcriptomic resources for this species are still lack- ing which is crucial to understand the molecular mechanisms associated with important traits such as growth, immune response, reproduction and sex determination. For the first time, we sequenced the transcriptome from a whole juve- nile fish using Illumina NovaSEQ60 0 0 generating raw paired- end reads. De novo transcriptome assembly generated a draft transcriptome (BUSCO5 completeness of 91.2% [Actinoptery- gii_odb10 database]) consisting of 259,403 putative tran- scripts with a total and N50 length of 333,881,215 bp and 2283 bp, respectively. A total count of 77,503 non-redundant protein coding sequences were predicted from the transcripts and used for functional annotation. We mapped the pre- dicted proteins to 304 known KEGG pathways with signal transduction cluster having the highest representation fol- lowed by immune system and endocrine system. In addi- tion, transcripts exhibiting significant similarity to previously published growth-and immune-related genes were identified which will facilitate future molecular breeding of Tor tambra

First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)

The sago palm (Metroxylon sagu Rottboll) is a tropical halophytic starch-producing, economically important crop palm mainly located in Southeast Asian countries. Recently, a genome survey was conducted on this palm using the Illumina sequencing platform, with a very low (21.5%) BUSCO genome completeness score, and most of them (∼78%) are either fragmented or missing. Thus, in this study, the sago palm genome completeness was further improved with the utilization of the Nanopore sequencing platform that produced longer reads. A hybrid genome assembly was conducted, and the outcome was a much complete sago palm genome with BUSCO completeness achieved at as high as 97.9%, with only ∼2% of them either fragmented or missing. The estimated genome size of the sago palm is 509,812,790 bp in this study. A sum of 33,242 protein-coding genes was revealed from the sago palm genome and around 96.39% of them had been functionally annotated. An investigation on the carbohydrate metabolism KEGG pathways also unearthed that starch synthesis was one of the major sago palm activities. The genome data obtained from this work is indispensable for future molecular evolutionary and genome-wide association studies on the economically important sago palm

Whole‑Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain

A Review on the Emerging Asian Aquaculture Fish, the MalaysianMahseer (Tor tambroides): Current Status and the Way Forward

The Malaysian mahseer (Tor tambroides)is a sport, ornamental and food all-in-one treasured aquaculture fish member of the Cyprinidae family. However, this freshwater riverine species is currently under the threats of habitat degradation and overfishing, apart from its poorly documented taxonomy. Despite its socio-economic significance, taxonomy confusion and conservation inadequacy, the knowledge gaps in some fields like the genomic landscape and biology are yet to be filled. In this comprehensive review, we presented an overview of all the past and current T. tambroides related research fields, namely morphology, population genetics, growth environment, reproduction, diet and nutrition, metagenome, mitogenome as well as conservation. Furthermore, we have included some future perspectives and recommendations for the advancement of the respective fields. It is anticipated that this review would be of great benefit to those planning to consolidate resources and work in tandem to pace the conservation and fish farming industry improvement endeavours

Microbiome analysis of gut bacterial communities of healthy and diseased Malaysian mahseer (Tor tambroides) using 16S rRNA metagenomics approach

Aims: The gut microbiota is referred to as an ‘extra organ’ and is critical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter the gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides. Methodology and results: In this study, such gut microbial alterations were explored using NGS-based 16S rDNA targeted sequencing on the Malaysian mahseer (T. tambroides). Three healthy adult and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulose degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides. Conclusion, significance and impact of study: Thus, our findings emphasized on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish

Metagenomic Analysis of Gut Bacterial Communities of Healthy and Diseased Empurau (Tor tambroides)

The gut microbiota is known as an ‘extra organ’ and is essential in assisting the host in terms of nutrition and immunity. Gut inflammation associated with bloom of Enterobacteriaceae and overgrowth of existing and invasion of pathogenic bacteria is mainly due to alteration in gut microbial community. This will eventually increases the disease occurrence within aquaculture farms which bring huge economic loses. However, the possible opportunistic pathogens causing bacterial disease is still in vague. Thus, in this study, the gut microbial community of both diseased and healthy Malaysian mahseer (T. tambroides) were compared and explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer. Three healthy and diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group, which is in coherent with diversity resistance hypothesis, indicating greater chances of occurrence for a species with antagonistic trait against pathogens. Analysis of Composition of Microbiomes (ANCOM) was performed to test on the significant differences at genus and phylum level among the gut microbiota between both groups. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio, Arcobacter and Pseudomonas were found within gut microbiota of the diseased fishes. In contrast, Sphingomonadaceae, Methylobacterium, unclassified bacteria and Ruminococcaceae were identified from the gut microbial community of the healthy group. Besides, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides as well. Taken together, our findings emphasised the association between the alteration in gut microbiota composition and infectious abdominal dropsy in T. tambroides, hoping to aid in diagnosis, prevention and treatment of intestinal diseases in fish

The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species

The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species

Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers

The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape