Genome assemblies for seven families of birds from the Global South

Abstract

Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads - Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores >97%, UCEs >4799). Repeat masking identified [~]10% of the genomes as interspersed repeats, and functional annotations yielded an average of 9,619 protein-coding genes per species. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxson test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.