De Novo Whole-Genome Sequencing and Assembly of the Yellow-Throated Bunting (Emberiza elegans) Provides Insights into Its Evolutionary Adaptation
by
, and
Tingli Hu
1, 
Guotao Chen
1,
Zhen Xu
1,
Site Luo
2,
Hui Wang
3,
Chunlin Li
4,
Lei Shan
5,* and
Baowei Zhang
1,* 1
School of Life Sciences, Anhui University, Hefei 230601, China
2
School of Life Sciences, Xiamen University, Xiamen 361102, China
3
College of Food and Bioengineering, Bengbu University, Bengbu 233030, China
4
School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
5
School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
*
Authors to whom correspondence should be addressed.
Animals 2022, 12(15), 2004; https://doi.org/10.3390/ani12152004
Submission received: 22 April 2022
/
Revised: 6 July 2022
/
Accepted: 4 August 2022
/
Published: 8 August 2022
(This article belongs to the Section Animal Genetics and Genomics)
Simple Summary
We report the genomic sequence of Emberiza elegans for understanding the evolutionary mechanisms of environmental adaptation and for studying a more effective genetic monitoring of this species. The E. elegans assembly was approximately 1.14 Gb, with a scaffold N50 of 28.94 Mb. About 15,868 protein-coding genes were predicted, and 16.62% of the genome was identified as having repetitive elements. Our genomic evolution analyses found considerable numbers of adaptive genes that may help the yellow-throated bunting cope with migratory behavior and environmental stressors of diseases. These results provide us with new insights into genomic evolution and adaptation, thus providing a valuable resource for further studies of population genetic diversity and genome evolution in this species.
Abstract
Yellow-throated bunting is a small migratory songbird unique to the Palearctic region. However, the genetic studies of this species remain limited, with no nuclear genomic sequence reported to date. In this study, the genomic DNA from the bird was sequenced in long reads using Nanopore sequencing technology. Combining short-read sequencing, the genome was well-assembled and annotated. The final length of the assembly is approximately 1.14 Gb, with a scaffold N50 of 28.94 Mb. About 15,868 protein-coding genes were predicted, and 16.62% of the genome was identified as having repetitive elements. Comparative genomic analysis showed numerous expanded gene families and positively selected genes significantly enriched in those KEGG pathways that are associated with migratory behavior adaptation and immune response. Here, this newly generated de novo genome of the yellow-throated bunting using long reads provide the research community with a valuable resource for further studies of population genetic diversity and genome evolution in this species.
Keywords:
adaptation; Emberiza elegans; genome; Nanopore sequencing
