High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl
An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a “Least Concern” conservation status and the latter is an “Endangered” species. To understand the genetic basis of this d...
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Elsevier
2023-08-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844023057791 |
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| author | Abhisek Chakraborty Samuel Mondal Shruti Mahajan Vineet K. Sharma |
| author_facet | Abhisek Chakraborty Samuel Mondal Shruti Mahajan Vineet K. Sharma |
| author_sort | Abhisek Chakraborty |
| collection | DOAJ |
| description | An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a “Least Concern” conservation status and the latter is an “Endangered” species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance such as NEO1 and UNC5, semaphorin (SEMA), and ephrin receptor showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of species-specific gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time. |
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| format | Article |
| id | doaj.art-a776463f939e4346a335d2b267913f8e |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-03-12T12:22:53Z |
| publishDate | 2023-08-01 |
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| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-a776463f939e4346a335d2b267913f8e2023-08-30T05:51:48ZengElsevierHeliyon2405-84402023-08-0198e18571High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowlAbhisek Chakraborty0Samuel Mondal1Shruti Mahajan2Vineet K. Sharma3MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, IndiaMetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, IndiaMetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, IndiaCorresponding author.; MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, IndiaAn intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a “Least Concern” conservation status and the latter is an “Endangered” species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance such as NEO1 and UNC5, semaphorin (SEMA), and ephrin receptor showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of species-specific gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.http://www.sciencedirect.com/science/article/pii/S2405844023057791Blue peafowlGreen peafowlGenome sequencingGenome assemblyPseudochromosomeAdaptive evolution |
| spellingShingle | Abhisek Chakraborty Samuel Mondal Shruti Mahajan Vineet K. Sharma High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl Heliyon Blue peafowl Green peafowl Genome sequencing Genome assembly Pseudochromosome Adaptive evolution |
| title | High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| title_full | High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| title_fullStr | High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| title_full_unstemmed | High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| title_short | High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| title_sort | high quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl |
| topic | Blue peafowl Green peafowl Genome sequencing Genome assembly Pseudochromosome Adaptive evolution |
| url | http://www.sciencedirect.com/science/article/pii/S2405844023057791 |
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