Scientists Successfully Assemble Chromosome-Scale Genome of Critically Endangered White-eared Night-Heron
In a groundbreaking accomplishment, researchers have achieved a major milestone in the field of genomics by successfully generating a high-quality reference genome of the critically endangered White-eared Night-Heron (Gorsachius magnificus) at the chromosomal level. This achievement was made possible through the integration of cutting-edge technologies, including PacBio long-read sequencing, chromosome conformation capture (Hi-C) technology, and Illumina platform paired-end short-read sequencing.
The assembled genome of the White-eared Night-Heron spans a total length of 1.176 Gb and is organized into 539 contigs and 79 scaffolds. The contig N50 length reached an impressive 18.46 Mb, while the scaffold N50 length was 84.77 Mb. Furthermore, the researchers utilized Hi-C technology to anchor 29 pairs of chromosomes, accounting for 99.89% of the assembled sequences, with a total length of 1.175 Gb.
This groundbreaking achievement has allowed the identification of 18,082 protein-coding genes utilizing both de novo and homolog-based strategies. Remarkably, 95% of these genes (17,177) were functionally annotated in publicly available databases such as Gene Ontology, KEGG, and Pfam. The researchers also conducted a BUSCO analysis, which demonstrated the completeness of 97.2% of the annotated genes.
Not only does this high-quality genome serve as a valuable reference for conservation genomics of the White-eared Night-Heron, but it also opens up avenues for phylogenomic and comparative genomic studies within the relatively understudied avian family, Ardeidae.
The scientific research conducted adhered to ethical guidelines and was conducted in accordance with the Chinese Animal Welfare Act (20090606) and approved by the Forestry Administration of Guangdong Province, China.
To attain the genome assembly, the researchers collected samples from a deceased male White-eared Night-Heron that had been housed at a wildlife rescue center in Shandong, Guangdong, China. Although sampling a female individual would have provided an opportunity to obtain the W chromosome, it was not feasible for this endangered and elusive species. Genomic DNA was extracted from muscle tissue for whole genome sequencing and subsequent de novo assembly. Additionally, nine RNA samples were obtained from various tissues within the same male individual for RNA sequencing analysis.
The researchers employed advanced techniques to extract high-molecular-weight genomic DNA from the muscle samples. They then utilized state-of-the-art sequencing technologies, including Illumina NovaSeq 6000 for whole genome survey and polishing, PacBio long-read sequencing for library construction, and Hi-C sequencing for capturing chromosomal interactions.
The resulting chromosome-scale reference genome was assembled through a comprehensive process involving the integration of PacBio long reads, Illumina short reads, and Hi-C sequencing data. It involved the initial draft contig assemblies, polishing of the draft genome, scaffolding using Hi-C data, and further adjustments to obtain the final chromosome-level assembly genome consisting of 79 scaffolds.
To ensure the quality and completeness of the genome assembly, BUSCO analysis was performed, which revealed high levels of completeness, with 96.6% of the BUSCO genes being complete. The researchers also annotated the genome by identifying repetitive sequences and conducting protein-coding gene predictions using various approaches, including transcriptome-based, homology-based, and de novo predictions.
Overall, this landmark achievement in genome assembly not only provides significant insights into the genetics of the critically endangered White-eared Night-Heron but also paves the way for further research in the field of conservation genomics and comparative genomics within the avian family, Ardeidae.
The research findings hold immense value for the scientific community and conservationists alike, as they offer new avenues for understanding and protecting this enigmatic and imperiled species.
