The first draft genome of Lophophorus: A step forward for Phasianidae genomic diversity and conservation

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications

BACKGROUND

High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa.

RESULTS

The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs).

CONCLUSIONS

A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.

A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation

The Tibetan Partridge (Perdix hodgsoniae) is an endemic species distributed in high-altitude areas of 3600-5600 m on the Qinghai-Tibet Plateau. To explore how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17 457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus), and Mikado Pheasant (Syrmaticus mikado). We found that 1014, 2595, and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs, respectively, of which 965 genes were common under positive selection with 3 different programs. Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while 6 gene families were under contraction. The total number of olfactory receptor genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on the evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms.

Characterization of highly polymorphic microsatellite markers for the chinese monal (Lophophorus lhuysii, Galliformes) using Illumina MiSeq sequencing

BACKGROUND

The Chinese monal (Lophophorus lhuysii, Galliformes) is a vulnerable and endemic bird from southwestern China. To better protect this species and increase its population size, genetic markers are urgently needed for investigation and conservation of both wild and captive populations.

METHODS AND RESULTS

By using next-generation sequencing, we developed and characterized markers for seven microsatellite loci of the Chinese monal. PCR examination and statistical analysis indicated that these microsatellites exhibited moderate to high levels of polymorphism, with the expected heterozygosity and polymorphic information content ranging from 0.578 to 0.858 and from 0.540 to 0.841, respectively. Cross-species genome comparison further suggests that these microsatellites are a feature of certain galliform species rather than being specific to the Chinese monal.

CONCLUSION

A combination of the seven highly polymorphic loci may provide a fundamental genetic toolkit to assess genetic backgrounds and will contribute to design conservation plan, breeding management and other possible studies of the Chinese monal and other evolutionarily related species in the future.

The De Novo Genome Sequencing of Silver Pheasant (Lophura nycthemera)

Silver pheasant (Lophura nycthemera) belongs to Phasianidae, Galliformes, which exhibits high subspecific differentiation. In this study, we assembled a novel genome based on 98.42 Gb of Illumina sequencing data and 30.20 Gb of PacBio sequencing data. The size of the final assembled genome was 1.01 Gb, with a contig N50 of 6.96 Mb. Illumina paired-end reads (94.96%) were remapped to the contigs. The assemble genome shows high completeness, with a complete BUSCO score of 92.35% using the avian data set. A total of 16,747 genes were predicted from the generated assembly, and 16,486 (98.44%) of the genes were annotated. The average length of genes, exons, and introns were 19,827.53, 233.69, and 1841.19 bp, respectively. Noncoding RNAs included 208 miRNAs, 40 rRNAs, and 264 tRNAs, and a total of 189 pseudogenes were identified; 116.31 Mb (11.47%) of the genome consisted of repeat sequences, with the greatest proportion of LINEs. This assembled genome provides a valuable reference genome for further studies on the evolutionary history and conversion genetics of L. nycthemera and the phylogenomics of the Galliformes lineage.

Exploring potentialities of avian genomic research in Nepalese Himalayas

Nepal, a small landlocked country in South Asia, holds about 800 km of Himalayan Mountain range including the Earth's highest mountain. Within such a mountain range in the north and plain lowlands in the south, Nepal provides a habitat for about 9% of global avian fauna. However, this diversity is underrated because of the lack of enough studies, especially using molecular tools to quantify and understand the distribution patterns of diversity. In this study, we reviewed the studies in the last two decades (2000‒2019) that used molecular methods to study the biodiversity in Nepal to examine the ongoing research trend and focus. Although Nepalese Himalaya has many opportunities for cutting-edge molecular research, our results indicated that the rate of genetic/genomic studies is much slower compared to the regional trends. We found that genetic research in Nepal heavily relies on resources from international institutes and that too is mostly limited to research on species monitoring, distribution, and taxonomic validations. Local infrastructures to carry out cutting-edge genomic research in Nepal are still in their infancy and there is a strong need for support from national/international scientists, universities, and governmental agencies to expand such genomic infrastructures in Nepal. We particularly highlight avian fauna as a potential future study system in this region that can be an excellent resource to explore key biological questions such as understanding eco-physiology and molecular basis of organismal persistence to changing environment, evolutionary processes underlying divergence and speciation, or mechanisms of endemism and restrictive distribution of species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s40657-021-00290-5.

The draft genome of the blood pheasant (Ithaginis cruentus): Phylogeny and high-altitude adaptation

The blood pheasant (Ithaginis cruentus), the only species in the genus Ithaginis, lives in an extremely inhospitable high-altitude environment, coping with hypoxia and ultraviolet (UV) radiation. To further investigate the phylogeny of Phasianidae species based on complete genomes and understand the molecular genetic mechanisms of the high-altitude adaptation of the blood pheasant, we de novo assembled and annotated the complete genome of the blood pheasant. The blood pheasant genome size is 1.04 Gb with scaffold N50 of 10.88 Mb. We identified 109.92 Mb (10.62%) repetitive elements, 279,037 perfect microsatellites, and 17,209 protein-coding genes. The phylogenetic tree of Phasianidae based on whole genomes revealed three highly supported major clades with the blood pheasant included in the "erectile clade." Comparative genomics analysis showed that many genes were positively selected in the blood pheasant, which was associated with response to hypoxia and/or UV radiation. More importantly, among these positively selected genes (PSGs) which were related to high-altitude adaptation, sixteen PSGs had blood pheasant-specific missense mutations. Our data and analysis lay solid foundation to the study of Phasianidae phylogeny and provided new insights into the potential adaptation mechanisms to the high altitude employed by the blood pheasant.

The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

The Sichuan partridge (Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.

Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)

The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.