Sequencing and assembly of the Egyptian buffalo genome

Abstract

Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done to reveal its genome structure and genomic traits. This is due to the complications stemming from the large genome size, the complexity of the genome, and the high repetitive content. In this paper, we introduce a high-quality draft assembly of the Egyptian water buffalo genome. The Egyptian breed is used as a dual purpose animal (milk/meat). It is distinguished by its adaptability to the local environment, quality of feed changes, as well as its high resistance to diseases. The genome assembly of the Egyptian water buffalo has been achieved using a reference-based assembly workflow. Our workflow significantly reduced the computational complexity of the assembly process, and improved the assembly quality by integrating different public resources. We also compared our assembly to the currently available draft assemblies of water buffalo breeds. A total of 21,128 genes were identified in the produced assembly. A list of milk virgin-related genes; milk pregnancy-related genes; milk lactationrelated genes; milk involution-related genes; and milk mastitis-related genes were identified in the assembly. Our results will significantly contribute to a better understanding of the genetics of the Egyptian water buffalo which will eventually support the ongoing breeding efforts and facilitate the future discovery of genes responsible for complex processes of dairy, meat production and disease resistance among other significant traits.

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

“…Mammalian genomes contain large families of repeats ( Goodier and Kazazian 2008 ), such as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and long-terminal repeats (LTRs). RepeatMasker revealed that 42.12% of the lowland anoa genome is composed of repetitive regions ( Table 7 ), which is comparable to data previously published for genome assemblies of river buffalo and other bovids ( Deng et al 2016 ; Low et al 2019 ; Mintoo et al 2019 ; El-Khishin et al 2020 ). Results also agree with the repetitive content in the cattle genome ( Fig.…”

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

“…RepeatMasker revealed that 42.12% of the lowland anoa genome is composed of repetitive regions (Table 7), which is comparable to data previously published for genome assemblies of river buffalo and other bovids (Deng et al, 2016; Low et al, 2019; Mintoo et al,. 2019; El-Khishin et al, 2020). Results also agree with the repetitive content in the cattle genome (Figure 7b).…”

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

“…Furthermore, the collected and presented ncRNA data shown in Table 1 use statistics from the NONCODE and GENCODE databases, originated from three main sources: (1) literature mining, (2) GenBank, and (3) specialized database such as Ensembl, RefSeq, lncRNAdb, lncipedia, LncRNADisease v2.0, etc. The other species, including cattle, use additional publication sources with updated genomic element profiles [108].…”