High-quality genome assembly of the endemic threatened White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 22, 2024

The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevational restricted species occurring in the Shola Sky Islands of Western Ghats India. This unique understory bird, with a complex vocal repertoire, exhibits impacts gene flow due to anthropogenic habitat fragmentation. Here, we present first genome assembly for Sholicola albiventris, which was assembled using combination Nanopore and Illumina sequences. final 1.083 Gbp, consisting 975 scaffolds N50 68.64Mbp L50 6. Our assembly's completeness supported by high number BUSCOs (99.9%) total 4887 ultraconserved element (UCE) loci retrieved. We also report complete mitochondrial comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs. identified 11.82% nuclear as repetitive 36,000 putative 12017 genes functionally annotated. showed great synteny between Taeniopygia guttata Gallus gallus chromosome level assemblies. reference will be pivotal investigating landscape connectivity, sub-population genetics, local adaptation, conservation genetics this high-elevation, range-restricted endemic bird species.

Language: Английский

---

High-Quality Genome Assembly of the Endemic, Threatened White-Bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) From the Shola Sky Islands, India

Published: Oct. 16, 2024

The White-bellied Sholakili (_Sholicola albiventris_) is an endemic, elevational restricted species occurring in the Shola Sky Islands of Western Ghats India. This unique understory bird, with a complex vocal repertoire, exhibits impacts gene flow due to anthropogenic habitat fragmentation. Here, we present first genome assembly for _Sholicola albiventris_, which was assembled using combination Nanopore and Illumina sequences. final 1.083 Gbp, consisting 975 scaffolds N50 68.64Mbp L50 6. Our assembly’s completeness supported by high number BUSCOs (99.9%) total 4887 ultraconserved element (UCE) loci retrieved. We also report complete mitochondrial comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs. identified 11.82% nuclear as repetitive 36,000 putative 12017 genes functionally annotated. showed great synteny between _Taeniopygia guttata_ _Gallus gallus_ chromosome level assemblies. reference will be pivotal investigating landscape connectivity, sub-population genetics, local adaptation, conservation genetics this high-elevation, range-restricted endemic bird species.

Language: Английский

---

Chromosome-level genome assembly of the European green woodpecker Picus viridis

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(5)

Published: March 27, 2024

Abstract The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled highly contiguous genome assembly for this using combination of short- and long-read sequencing scaffolded with chromatin conformation capture (Hi-C). final was 1.28 Gb features scaffold N50 37 Mb L50 39.165 Mb. incorporates 89.4% genes identified birds OrthoDB. Gene repetitive content annotation on detected 15,805 ∼30.1% occurrence elements, respectively. Analysis synteny demonstrates fragmented nature P. viridis when compared to chicken (Gallus gallus). annotations produced study will certainly help further research into genomics comparative evolution woodpeckers. Five historical seven contemporary samples have been resequenced may give insights population history species.

Language: Английский

---

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(6)

Published: April 12, 2024

The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. discoveries the hind limbs basal and dinosaurs have sparked an interest in evolutionary origin genetic mechanism feathered However, majority studies investigating genes associated with this trait focused domestic populations. Understanding underpinned feathered-foot development wild still its infancy. Here, we assembled chromosome-level genome Asian house martin (Delichon dasypus) using long-read High Fidelity sequencing approach to initiate search for We employed whole-genome alignment D. dasypus other swallow species identify high-SNP regions chromosomal inversions genome. After filtering out variations unrelated evolution, found six related near regions. also detected three between barn genomes. discussed association wingless/integrated (WNT), bone morphogenetic protein, fibroblast growth factor pathways potential roles development. Future are encouraged utilize explore process avian species. This endeavor will shed light path birds.

Language: Английский

---

Chromosome-level genome assembly of the European Green woodpeckerPicus viridis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 20, 2023

Abstract The European Green Woodpecker, Picus viridis , is a widely distributed species found in the Western Palearctic region. Here we assembled highly contiguous genome assembly for this using combination of short and long reads sequencing scaffolded with chromatin conformation capture (Hi-C). final was 1.28 Gb features scaffold N50 37Mb L50 39.165 Mb. incorporates 89.4% genes identified birds OrthoDB. Gene repetitive content annotation on detected 15,805 ∼30.1% occurrence elements, respectively. Analysis synteny demonstrates fragmented nature when compared to chicken ( Gallus gallus ). annotations produced study will certainly help further research into genomics P. comparative evolution woodpeckers.

Language: Английский

---