Sequencing and assembly of the Egyptian buffalo genome

Influence of sugarcane bagasse on in vitro degradability, rumen characteristics, nutrients digestibility, blood parameters and milk production of lactating buffaloes

This study aimed to evaluate the use of sugarcane bagasse (SCB) as exclusive roughage in lactating buffaloes on digestibility, milk production and composition, and microbial protein. In vitro dry matter digestion (IVDMD) and organic matter digestion (IVOMD) for SCB as a replacement for barley straw (BS) of the control ration have been determined. In vivo experiment, 55 lactating buffaloes were randomly assigned into five groups. First group was fed the control ration (60% concentrate feed mixture (CFM) and 40% BS), second group was fed 60% CFM and 30% BS + 10% SCB, third group was fed 60% CFM and 20% BS + 20% SCB, fourth group was fed 60% CFM and 10% BS + 30% SCB and fifth group was fed 60% CFM and 40% SCB. Results indicated that IVDMD% and IVOMD% degradability were increased with the inclusion SCB in rations compared with the control. Full replacement of BS by SCB 40% significantly (p < 0.05) increased nutrients digestibility coefficient with improving ruminal basic parameters. Buffaloes fed SCB40 had higher milk component yields, 4% fat corrected milk and plasma proteins, and lower plasma creatinine and cholesterol than control buffaloes (p < 0.05). Finally, the inclusion of SCB up to 40% in lactating buffaloes rations favorably affected rumen fermentation characteristics (in vitro) and improved nutrients digestibility and milk production (in vivo).

Exploring virus presence in field-collected potato leaf samples using RNA sequencing

BACKGROUND

The quick and accurate identification of viruses is essential for plant disease management. Next-generation sequencing (NGS) technology may allow the discovery, detection, and identification of plant pathogens. This study adopted RNA-sequencing (RNA-Seq) technology to explore the viruses in three potato plants (S3, S4, and S6) growing under field conditions.

RESULTS

Potato-known infecting viruses, such as alfalfa mosaic virus (AMV), potato leafroll virus (PLRV), and potato virus Y (PVY), were identified using bioinformatics programs and validated using RT-PCR. The presence of these potato viruses was also confirmed by visual inspection of host symptoms. In addition, the nearly complete genome of PLRV and the complete or partial genome sequence of multipartite virus segments have been identified. Besides the three major potato viruses that BLASTn analysis revealed were present in our samples, BLASTx analysis revealed some reads are derived from other potato viruses, such as potato virus V (PVV), Andean potato latent virus (APLV), and tomato chlorosis virus (ToCV), which are not frequently reported in potato field screenings in Egypt. Other microbial agents, such as bacteria and fungi, were also identified in the examined sample sequences. Some mycovirus sequences derived from ourmia-like viruses and Alternaria alternata chrysovirus were also identified in sample S4, confirming the complexity of the potato microbiome under field conditions.

CONCLUSION

NGS quickly and accurately identifies potato plant viruses under field conditions. Implementing this technology on a larger scale is recommended to explore potato fields and imported plants, where symptoms may be absent, unspecific, or only triggered under certain conditions.

Efficacy of Duddingtonia flagrans (Bioverm®) on the biological control of buffalo gastrointestinal nematodes

We evaluated the efficacy of Bioverm®, a commercial product containing Duddingtonia flagrans, on the control of buffalo (Bubalus bubalis) gastrointestinal nematodes. We randomly divided 12 buffaloes into two groups of six animals. In the treated group, each animal received a Bioverm®`s single dose of 1g (105 chlamydospores of D. flagrans) to 10 kg of live weight; in the control group, each animal received 1g of corn bran for each 10 kg of live weight as a placebo. Fecal samples were individually collected from 12, 24, 36, 48, 60 and 72 h after treatments. To examine 1) viability of chlamydospores passed through the gastrointestinal tract, 2 g of faeces and 1000 infective larvae (L3) were added to Petri dishes with 2% water-agar, and 2) to examine larval predation by D. flagrans during fecal cultures, 2000 L3 were added. In the Petri dishes, were observed significant reductions (p < 0.01) in the treated group after 48 (56.7%) and 60 h (91.5%). In the fecal cultures, significant reductions (p < 0.01) occurred in the treated group from 36 h (75%), with larval reduction up to 72 h. High larval predation rate occurred 60 h after Bioverm® administration. Bioverm® maintained viability and predation capacity after passage through the buffalo's gastrointestinal tract, showing efficacy on gastrointestinal nematodes.

Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review

Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.

Genome-wide identification of bovine ADAMTS gene family and analysis of its expression profile in the inflammatory process of mammary epithelial cells

ADAM metallopeptidase with thrombospondin type 1 motif (ADAMTS) are secreted, multi-domain matrix-related zinc endopeptidases that play a role in organogenesis, assembly and degradation of extracellular matrix (ECM), cancer and inflammation. Genome-wide identification and analysis of the bovine ADAMTS gene family has not yet been carried out. In this study, 19 ADAMTS family genes were identified in Bos taurus by genome-wide bioinformatics analysis, and they were unevenly distributed on 12 chromosomes. Phylogenetic analysis shows that the Bos taurus ADAMTS are divided into eight subfamilies, with highly consistent gene structures and motifs within the same subfamily. Collinearity analysis showed that the Bos taurus ADAMTS gene family is homologous to other bovine subfamily species, and many ADAMTS genes may be derived from tandem replication and segmental replication. In addition, based on the analysis of RNA-seq data, we found the expression pattern of ADAMTS gene in different tissues. Meanwhile, we also analyzed the expression profile of ADAMTS gene in the inflammatory response of bovine mammary epithelial cells (BMECs) stimulated by LPS by qRT-PCR. The results can provide ideas for understanding the evolutionary relationship and expression pattern of ADAMTS gene in Bovidae, and clarify the theoretical basis of the function of ADAMTS in inflammation.

Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly and made comparison to published buffalo genomes. The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 and 19.83 kbp, respectively, mean coverage was 44× and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (1) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo and (2) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic features. De novo gene predictions identified 32,393 genes, representing 97.14% of the reference’s annotated genes, whilst BUSCO search against the mammalian orthologs database identified 71.1% complete, 11.7% fragmented, and 17.2% missing orthologs, indicating a good level of completeness for downstream analyses. Repeat analyses indicated that the lowland anoa genome contains 42.12% of repetitive regions. The genome assembly of the lowland anoa is expected to contribute to comparative genome analyses among bovid species.

Genomics of Adaptations in Ungulates

Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.