The checklist was based upon the most relevant standards, recognized scientific findings, and the institute's own observations on machinery. Based upon the results of this project, BGI Parts 1 and 2 were published in Since rules and findings in this area are changing dynamically, regular updates were planned from the outset. The download statistics for the checklist are indicative of strong demand. The structure of the checklist and of all associated documents was retained.
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As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus , golden pheasant Chrysolophus pictus and Lady Amherst's pheasant Chrysolophus amherstiae , exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds.
We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15, protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration.
By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively.
In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis.
Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity. The plumage colors of birds serve functions in crypsis, social signaling, and mate choice [ 1 ].
Due to the diversity of colors and ease of observation, plumage provides an ideal model to explore the formation and genomic evolution of coloration patterns in animals. Studies on birds and mammals suggest that the integument colors are regulated by several mechanisms.
Melanin, which is produced by neural crest cell-derived melanocytes, is a major contributor to pigmentation in avian feathers and mammalian hairs [ 2 ]. Black and brown feathers are derived from the deposition of eumelanin, whereas reddish and light-yellow feathers are due to pheomelanin.
Carotenoids are chemicals for vitamin synthesis and act as antioxidants for the immune system [ 2 ]. Red colors may also come from other rare pigments, such as porphyrins in black-shouldered kites [ 4 ], psittacofulvins in parrots [ 5 ], iron oxide in Gypaetus barbatus , and turacin in Tauraco macrorhynchus [ 6 ].
In addition, feather coloration may also be a result of specific structures that combine with noniridescent colors and iridescent metal lusters [ 2 ].
Feather complex coloration is likely coordinated through multiple genes that regulate diverse mechanisms. The melanogenesis biosynthetic pathway has been elucidated [ 7 , 8 ], and previous studies have revealed the DNA polymorphisms of several genes that lead to variations in melanin-based coloration [ 9 ]. Some candidate genes for carotenoid-related functions in mammals and invertebrates have been documented, and their homologous genes may also be present in birds [ 11 ].
However, the production metabolism of carotenoid pigments has not been well characterized. Additionally, the nanostructural colors of feathers are related to keratinization and affected by keratin genes [ 12 , 13 ]. Genome information could provide new perspectives to study the mechanisms of bird coloration. However, this work included only 15 genes without distinguishing melanin, carotenoid, or other pigments. Thus, further studies are necessary to investigate the candidate molecular mechanisms of avian plumage coloration.
In the present study, we focused on the plumage coloration issues of golden pheasant Chrysolophus pictus at the genome and transcriptome levels, together with its sister species, the Lady Amherst's pheasant Chrysolophus amherstiae. These species are two important organisms for studies of plumage coloration because of their phenotypic differences and close relationship.
These two species can even crossbreed to produce fertile offspring under human feeding conditions. In adult male golden pheasant, both the crest and rump feathers are golden-yellow in color, the belly and upper tail coverts are dark red, the nape feathers are light orange with two black stripes, the mantle is iridescent green, and the tail is black spotted with cinnamon Fig.
The golden pheasant is a colorful avian species with distinct brilliant feather colors in adult males, which can be observed with obvious characteristics of melanin and carotenoid pigments. By comparison, adult male Lady Amherst's pheasants have red and yellow feathers exclusively distributed over small parts of the body, including the crest, rump, and upper tail coverts, while most of the other body parts are white or black Fig.
Carotenoids were present in the yellow back feathers of golden pheasant, but it was unclear whether they were present in Lady Amherst's pheasant [ 17 ].
In the present study, we sequenced the genome and transcriptome of these two pheasants and identified the melanin and carotenoid pigments in plumages of the two pheasant species by using high-performance liquid chromatography HPLC and Raman spectroscopy RS methods.
Then, we conducted a comprehensive comparative analysis with 51 other sequenced avian references [ 15 , 18 , 19 ] at a suitable level to investigate the evolution of the plumage coloring of golden pheasant or Chrysolophus.
Profile of golden pheasant upper right and Lady Amherst's pheasant upper left and their feathers from different body parts lower part. Both male species near are more colorful than females far. The female feathers are represented by the napes. A series of paired-end libraries with different insert sizes were constructed and sequenced by using the Illumina Hiseq platform Supplementary Table S1. The de novo assembly size was 1. These reads covered In addition, the assembly covered more than To obtain a global view of potential specific elements in golden pheasant, We identified 7.
Moreover, the golden pheasant genome was used as a reference to align the transcriptome sequences from these two species. The average mapping rates of golden pheasant and Lady Amherst's pheasant are These results imply a close relationship between these two species. Comparative genomic analyses among the golden pheasant and other avian species.
The tree was constructed based on , bp 4-fold degenerate sites, from 6, single-copy orthologous genes among six sequenced Galliformes genomes golden pheasant, chicken, turkey, Japanese quail, northern bobwhite, and scaled quail , the sequenced Anseriformes duck , and the zebra finch as outgroup. The background species are selected based on Galliformes species and Jarvis's phylogeny for the 48 avian genomes [ 16 ], of which 11 birds with high quality of genome build from 10 different clades are selected in this analysis.
Combining the homology-based and transcriptome-assisted methods, 15, protein-coding genes were identified in the assembly of golden pheasant, of which Moreover, repetitive elements REs comprised approximately The expanded satellite DNAs in the golden pheasant genome were 5.
S3 and Table S7. Increasing evidence has suggested that TEs might play a role as candidate gene expression regulators, especially in the modulation of abutting gene expression [ ]. Thus, genes within 2 kb up- and downstream of these TEs were examined. Functional enrichment showed that the specific or expanded REs may be involved in the adaptive evolution of golden pheasant or turkey.
The phylogenetic placement is a critical background for many comparative genomic analyses. To assess the phylogenetic position of the golden pheasant in Galliformes, a phylogenetic tree was constructed with five other sequenced Galliformes chicken [ 23 ], turkey [ 24 ], Japanese quail [ 18 ], northern bobwhite,[ 19 ] and scaled quail [ 19 ] ; the sequenced Anseriformes duck [ 25 ] , which is closest to Galliformes; and a model species zebra finch [ 26 ] as an outgroup.
The phylogenetic analysis of 48 birds concluded that protein-coding genes might reflect life history traits more than phylogeny topology would [ 16 ]. Therefore, we constructed the phylogeny tree using , 4-fold degenerate 4D sites from 6, one-to-one orthologous genes that are sites that do not change the amino acid and are typically considered to be less subject to selective pressure. The result showed that the golden pheasant is taxonomically closer to turkey than to chicken Fig. The relationship was consistent with the above REs analysis that golden pheasant and turkey had similar divergence distribution Supplementary Fig.
This phylogeny was also uncontroversial with a previous study that was based on six nuclear intron sequences and two mitochondrial regions [ 27 ]. Furthermore, the divergence time of the golden pheasant and turkey was estimated approximately 13 million years ago Mya by using MCMCTree Fig.
Identifying these variations may provide clues for the next investigations. Positive Darwinian selection is a universal strategy to identify candidates of adaptive evolution at the DNA sequence level.
For the 6, one-to-one orthologous genes in eight birds, positive selected genes were identified in golden pheasant by using branch site model Supplementary Tables S8 and S9. For the multicopy gene families, lineage-specific gene families were identified in golden pheasant Fig.
Additionally, we identified expanded and 18 contracted gene families through a maximum likelihood framework Supplementary Tables S10 and S It is noteworthy that cytochrome P family 2 subfamily D member 6 CYP 2 D 6 was duplicated to three copies in the golden pheasant genome Fig. S6 , whereas only one copy was found in 48 other birds [ 16 ]. Although multiple copies of this gene are present in northern bobwhite and scaled quail, it is likely that independent duplication events occurred in the two Odontophoridae species and golden pheasant, respectively, based on our phylogeny Fig.
The CYP enzymes were considered good candidates for carotenoid ketolases [ 29 ]. Recently, a comparative analysis among 65 bird genomes revealed the CYP 2 J 19 gene, which belonged to the same clan as that of CYP 2 D and was a carotenoid ketolase functional in synthesizing red carotenoids from yellow carotenoids [ 30 ], and two other population studies revealed the CYP 2 J 19 was associated with red carotenoid-based coloration phenotypes in zebra finches and canaries [ 29 , 31 ].
Compared with other non-carotenoid Galliformes, copy number and protein sequence of CYP 2 J 19 in golden pheasant are conserved the sequence is more similar to that of the turkey.
However, the expression of CYP 2 J 19 in the orange nape of golden pheasant was significantly higher than other colored feathers. It could be suggested that CYP 2 J 19 might influence coloration at the transcriptional level in Chrysolophus. The expanded CYP 2 D 6 genes in golden pheasant may function in metabolism or biotransformation of some foreign chemicals and could be a candidate for carotenoid deposition in its feathers.
Melanin is the most common and widespread pigment in avian feathers and yields black, gray, brown, rufous, and buff shades and patterns [ 2 ]. Both Chrysolophus species possessed darker eumelanic and brighter pheomelanic colors in their integument plumage, particularly the most impressive bright red and yellow feathers in male individuals Fig. A previous investigation concluded that human hairs with six different colors, varying from black to brown to red, all contained both eumelanin and pheomelanin and that their proportions determined the visual colors.
The eumelanin content and proportions were the highest in black hairs, while red hairs contained comparable levels of eumelanin and pheomelanin [ 34 ]. We identified the lineage-specific varied genes in Chrysolophus by making comparisons with the five other Galliformes species and 11 additional birds with high quality of genome build that belong to 11 different clades in the phylogeny tree of the 48 birds [ 16 ].
S9 , and KIT has a two-amino acid deletion in the C-terminal region, which is conserved in other birds and even in green anole Supplementary Fig.
Melanogenesis is under multiple levels of complex regulation, mainly through the transcriptional and post-transcriptional regulation of the MITF gene, which can stimulate the transcription of genes that function in producing melanin [ ]. The lineage-specific varied genes in Chrysolophus are marked by a red star.
The significant higher expressed genes in feathers with green, red, and yellow color are marked by the colorful rectangle, respectively; all use the white feathers A-F-Nape and A-F-Belly as control.
A base of adenine inserts after the initiation codon of the open reading frame at exon 2A. This insertion was verified in another five Chrysolophus individuals lower part.
The upper section shows the alternative splicing models of ASIP. Rectangles represent exons, and curves represent junctions between the exons. The size scale ratio between exons and introns is The lower section is the expression the histogram of the junctions. Reads per million mapped reads was used to normalize expression levels. The color of the column matches the accepter exon color. The color of the footstone matches the donor exon color.
Descriptions are that same as in c.
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As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus , golden pheasant Chrysolophus pictus and Lady Amherst's pheasant Chrysolophus amherstiae , exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds. We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15, protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage.
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