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Phylogenetic position of peacock with respect to other bird genomes. The phylogenetic tree constructed from the concatenated alignments of the orthologous genes across all six species. The divergence time of different bird species was determined using the TimeTree database (Hedges et al., 2006), which is based on the published reports of molecular and fossil data. The origin of turkey was estimated to be ∼37.2 MYA, whereas the origin of peacock and chicken was estimated to be ∼32.9 MYA. The original phylogeny from the data had a polytomy due to which the split point between zebra finch and flycatcher could not be identified. However, for the sake of correct visual interpretation the divergence point between flycatcher and zebra finch (∼44 MYA) was identified using the TimeTree database. The values mentioned in Red are the branch length values and the values mentioned in Black are the phylogenetically corrected branch-specific ω or dN/dS values.
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The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra...
Citations
... ,128 .Genes with all three signatures of adaptive evolution The three evolutionary signatures of adaptation considered were higher evolution rate, positive selection, and unique amino acid substitutions with functional impact. T. cordifolia genes that indicated two of the three evolutionary signatures were suggested as genes with multiple signatures of adaptive evolution (MSA)118,124,[141][142][143] . The T. cordifolia genes showing all three signatures were considered genes with three signatures of adaptive evolution. ...
Tinospora cordifolia (Willd.) Hook.f. & Thomson, also known as Giloy, is among the most important medicinal plants that have numerous therapeutic applications in human health due to the production of a diverse array of secondary metabolites. To gain genomic insights into the medicinal properties of T. cordifolia, the genome sequencing was carried out using 10× Genomics linked read and Nanopore long-read technologies. The draft genome assembly of T. cordifolia was comprised of 1.01 Gbp, which is the genome sequenced from the plant family Menispermaceae. We also performed the genome size estimation for T. cordifolia, which was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed. The genome and transcriptome assemblies were used to construct the gene set, resulting in 17,245 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also positioned as basal eudicot by constructing a genome-wide phylogenetic tree using multiple species. Further, a comprehensive comparative evolutionary analysis of gene families contraction/expansion and multiple signatures of adaptive evolution was performed. The genes involved in benzyl iso-quinoline alkaloid, terpenoid, lignin and flavonoid biosynthesis pathways were found with signatures of adaptive evolution. These evolutionary adaptations in genes provide genomic insights into the presence of diverse medicinal properties of this plant. The genes involved in the common symbiosis signalling pathway associated with endosymbiosis (Arbuscular Mycorrhiza) were found to be adaptively evolved. The genes involved in adventitious root formation, peroxisome biogenesis, biosynthesis of phytohormones, and tolerance against abiotic and biotic stresses were also found to be adaptively evolved in T. cordifolia.
... 11.575009 doi: bioRxiv preprint In this context, the quality of reference genome assemblies benefited from the combination of Illumina short-read sequencing with third-generation sequencing platforms such as Pacific Bioscience (PacBio) 11 or Oxford Nanopore Technologies (ONT) 12 . Application of these technologies improved contiguity, completeness, and accuracy compared to assemblies based on short-read sequencing alone 13,14 . In general, the number of contigs and scaffolds was significantly reduced, and N50 values increased, leading to better genome annotation and identification of more genes, including non-coding RNA genes, pseudogenes, and transposable elements 15,16 . ...
The red-legged partridge, Alectoris rufa (n=38 chromosomes) plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of it genome (115 scaffolds, L90=23). This assembly contains 96.9% (8078 out of 8332) orthologous genes from the BUSCO aves_odb10 dataset of single copy orthologous genes. We identify RNA and protein genes, 95% of which with functional annotation. This near-chromosome level assembly revealed significant chromosome rearrangements compared to quail ( Coturnix japonica ) and chicken ( Gallus gallus ), suggesting that A. rufa and C. japonica diverged 21 M-years ago and that their common ancestor diverged from G. gallus 37 M-years ago. The reported assembly is a significant step towards a complete reference genome for A. rufa , contributing to facilitate comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.
... The advancement of the genomic era also allows researchers to assess genetic make-up, compare genetic diversity parameters between wild populations and captive species, and develop molecular markers as parameters for preserving genetic diversity and inbreeding issues [10][11][12][13]. The accessibility of these data can be advantageous for calculating harvest rates as well as managing or the translocation of wild birds for applications of wildlife management and conservation [5,14]. ...
... It has been reported that the Indian peafowl may serve as an indicator of changing climate conditions [33]. Furthermore, changes in climate patterns have been linked to the diminishing green peafowl population [10,16]. Historical climate change has caused a significant reduction in their population as it has been indicated that climate-induced changes in range during the Pleistocene-Holocene transition had an impact on the green peafowl [10,16]. ...
... Furthermore, changes in climate patterns have been linked to the diminishing green peafowl population [10,16]. Historical climate change has caused a significant reduction in their population as it has been indicated that climate-induced changes in range during the Pleistocene-Holocene transition had an impact on the green peafowl [10,16]. Notably, wild species have evolved as a response to shifts in climate conditions [40]. ...
Aves ranks among the top two classes for the highest number of endangered and extinct species in the kingdom Animalia. Notably, the IUCN Red List classified the green peafowl as endangered. This highlights promising strategies using genetics and reproductive technologies for avian wildlife conservation. These platforms provide the capacity to predict population trends and enable the practical breeding of such species. The conservation of endangered avian species is facilitated through the application of genomic data storage and analysis. Storing the sequence is a form of biobanking. An analysis of sequence can identify genetically distinct individuals for breeding. Here, we reviewed avian genomics and stem cell approaches which not only offer hope for saving endangered species, such as the green peafowl but also for other birds threatened with extinction.
... Using previously published re-sequencing (Jaiswal et al. 2018;Dong et al. 2021;Zhang et al. 2022) datasets, we identified population structure corresponding to geographic distribution within the green peafowl. These populations have different demographic histories, allegedly resulting Fig. 13). ...
The green peafowl (Pavo muticus, Linnaeus 1766) is an endangered species native to Southeast Asia. Despite considerable morphological diversity, the intraspecific genetic structure of green peafowl has not been comprehensively addressed. We used public whole-genome sequencing data of one blue and 52 green peafowls to characterise their genetic diversity, differentiation, identify Ancestry Informative Markers (AIMs) and compare their demographic histories. We found evidence of substantial population structure, with at least three distinct clusters and diverse demographic histories that may result from different responses to biogeoclimatic events. The genetic structure of native populations follows the pattern of the geographic distribution of the green peafowl with the highest autosomal pairwise FST between Yunnan and Vietnam (~ 0.1) and intermediate estimates for Thailand comparisons (~ 0.077). We identify AIMs to distinguish between these three native populations. The captive green peafowls from Xinxing clustered with Vietnam, and those from Qinhuangdao (QHD) formed a separate cluster. The two QHD individuals appear to have varying levels of blue peafowl ancestry based on PCA and admixture analysis and are mirrored in their demographic histories. Our study establishes the occurrence of genetically distinct natural populations of green peafowl that can be considered separate management units (MU) when planning conservation actions.
... Peacocks have intrigued biologists for hundreds of years and are still a fascinating specimen of study [3,4]. From Charles Darwin's explanation for the colourful plumage indicating that the vibrant plumage was selected sexually, to Amotz Zahavi proposing his handicap theory [1], a lot has been added to the understanding of peacock's unique pattern of evolution, still it remains among the most intriguing birds. ...
... The native habitat of green peafowl was spread across South East Asia, however this species is now extinct or near extinct in Malaysia, Bangladesh, and India, and is also facing reduction in population size in Thailand, Laos, China, and Indonesia [12,13]. Genomic, anthropogenic, and climatic evidences also suggest the decrease in effective population size or endangerment of green peafowl species, and the role of human disturbance in it [3,14]. Habitat loss has confined this species to restricted geographical regions, which caused a reduction in gene flow and higher rate of inbreeding [14]. ...
... Blue peafowl has been categorized as species of "Least Concern" whereas green peafowl has been declared as "Endangered" by IUCN for its gradual decrease in population size [15]. The first genome sequencing of blue peafowl (1.16 Gbp) performed by Jaiswal et al. (2018) [3] showed adaptive evolution of genes related to immunity, skeletal muscle, and feather development that aids in phenotypic evolution of blue peafowl, followed by the genome sequencing of this species by other groups [16,17]. The recent genome sequencing of green peafowl revealed a genome size of 1.05 Gbp consisting of 27 pseudochromosomes [14,18]. ...
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.
... Gene duplications and the neofunctionalization of genes have occurred in multiple vertebrate immune system gene families (e.g., MHC, NLPRP3, CD22, immunoglobins, TLRs, and SSC4D) [126,131,132]. Among the most studied gene families are immune pattern recognition receptors, and TLR gene family is of particular interest due to their involvement in pathogen detection. ...
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
... Other components of the MAC may have adapted to the loss of C9 to increase the efficiency of the C9 deficient MAC. For instance, several lineage-specific amino acid changes in complement components C5 and C8α have been reported in the Indian peacock (Jaiswal et al., 2018). How these lineage-specific changes affect function will require further studies. ...
The cytolytic activity of the membrane attack complex (MAC) is pivotal in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrate C6 gene. The subsequent duplication and divergence of this vertebrate C6 gene formed the C7, C8α, C8β, and C9 genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered that C9 has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at the C9 locus. In this study, we have generated a > 120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of the C9 gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons of C9 in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred after C9 gene loss in an early galliform ancestor. Loss of C9 in galliform birds, in contrast to conservation in other vertebrates, may have implications for host-pathogen interactions. Our study of C6 gene birth in an early vertebrate ancestor and C9 gene death in galliform birds provides insights into the evolution of the TCP.
... Other components of the MAC may have adapted to the loss of C9 to increase the efficiency of the C9 deficient MAC. For instance, several lineage-specific amino acid changes in complement components C5 and C8α have been reported in the Indian peacock (Jaiswal et al., 2018). How these lineage-specific changes affect function will require further studies. ...
The cytolytic activity of the membrane attack complex (MAC) has a crucial role in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrate C6 gene. The subsequent duplication and divergence of this vertebrate C6 gene formed the C7, C8 α , C8 β , and C9 genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered that C9 has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at the C9 locus. In this study, we have generated a >120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of the C9 gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons of C9 in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred after C9 gene loss in an early galliform ancestor. Our study of C6 gene birth in an early vertebrate ancestor and C9 gene death in galliform birds provides insights into the evolution of the TCP.
... The first draft of Indian peafowl genome assembly was released in 2018. However, the length of scaffold and contig N50 of the assembly were only 25.6 and 19.3 kb, respectively [15]. Subsequently, Dhar et al. improved the Indian peafowl genome using Illumina and Oxford Nanopore technology, and the length of scaffold N50 was determined up to 0.23 Mb [16]; however, the assembly quality still needed improvement. ...
... Gb of sequencing data on a 10X Genomics sequencing platform, and 110.74 Gb of sequencing data using the PacBio sequencing platform (Supplementary Table S1). In total, 387.34 Gb of sequencing data and a total coverage of 362× was obtained from the 3 sequencing strategies with the lengths of contig N50 and scaffold N50 separately up to 6.2 and 11.4 Mb, respectively, which exhibited a 50-fold improvement in the scaffold N50 compared to the previously published Indian blue peafowl genome reported by Jaiswal et al. [15] and Dhar et al. [16] (Fig. 2, Table 1, and Supplementary Table S2). The distribution of 17-mer showed a major peak at 154× (Supplementary Fig. S3). ...
... The results show that the Galliformes order is clustered, within which the Phasianidae family formed a group. Moreover, peafowl were found to be closer to turkey than chicken in the Phasianidae family; these findings are inconsistent with those reported by Jaiswal et al. [15]. We found that the relationship of chicken and quail was closer than turkey; white duck, belonging to the Anseriformes order, was closer to the Galliformes order (Fig. 3C). ...
Background
The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl.
Results
A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl.
Conclusions
This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.
... Ab initio annotation of repeats is necessary to gain a true understanding of genomic repetitive content, especially in nonmodel species (Platt et al. 2016). Unfortunately, many papers describing avian genomes (Cornetti et al. 2015;Laine et al. 2016;Jaiswal et al. 2018) only carry out homology-based repeat annotation using the Repbase (Bao et al. 2015) library compiled from often distantly related model avian genomes (mainly chicken and zebra finch). This lack of ab initio annotation can lead to the erroneous conclusion that TEs are inactive in newly sequenced species (Platt et al. 2016). ...
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
