Genome Assembly and Evolutionary Analysis of the Mandarin Duck <i>Aix galericulata</i> Reveal Strong Genome Conservation among Ducks

Ng, Chen Siang; Lai, Courteney K.; Ke, Huei-Mien; Lee, Hsin‐Han; Chen, Chih‐Feng; Tang, Pin‐Chi; Cheng, Hsu-Chen; Lu, Mei-Yeh Jade; Li, Wen-Hsiung; Tsai, Isheng Jason

doi:10.1093/gbe/evac083

Cited by 3 publications

(1 citation statement)

References 122 publications

(142 reference statements)

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“…1 ). After several rounds of molting, diverse feathers are derived from the juvenile feather follicles in the secondary transition process, as seen in the sail-feathers of the mandarin duck ( Aix galericulata ) or colorful contour feather of the pheasants 8 , 20 , 66 , 67 . The conserved primary feather transition suggests its functional importance for survival while the following diverse feather transitions are mainly for mating choices.…”

Section: Discussionmentioning

confidence: 99%

Transition from natal downs to juvenile feathers: conserved regulatory switches in Neoaves

Li,

Chuong,

Chen

et al. 2023

Preprint

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The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We discovered that LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial - mesenchymal interactions for branching morphogenesis. ACTA2 compartments dermal papilla stem cells for feather cycling. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We found this primary feather transition largely conserved in chicken (precocious) and zebra finch (altricial) and discussed the possibility that this evolutionary adaptation process started in feathered dinosaurs.

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Section: Discussionmentioning

confidence: 99%

Transition from natal downs to juvenile feathers: conserved regulatory switches in Neoaves

Li,

Chuong,

Chen

et al. 2023

Preprint

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Conserved regulatory switches for the transition from natal down to juvenile feather in birds

Chen,

Chang,

Jiang

et al. 2024

Nat Commun

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The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We report that extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial-mesenchymal interactions for branching morphogenesis. α-SMA (ACTA2) compartmentalizes dermal papilla stem cells for feather renewal cycling. LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We show that this primary feather transition is largely conserved in chicken (precocial) and zebra finch (altricial) and discuss the possibility that this evolutionary adaptation process started in feathered dinosaurs.

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Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

Safaa,

Khaled,

Isaac

et al. 2023

Journal of Genetic Engineering and Biotechnology

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Background Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. Results The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. Conclusion The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.

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Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks

Cited by 3 publications

References 122 publications

Transition from natal downs to juvenile feathers: conserved regulatory switches in Neoaves

Transition from natal downs to juvenile feathers: conserved regulatory switches in Neoaves

Conserved regulatory switches for the transition from natal down to juvenile feather in birds

Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

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