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Bos indicus is a domestic cattle species with many indigenous breeds found in India and is important for dairy, draught work, and other household activities. Distinct phenotypic differences are observed among the breeds of this species; however, their whole genome sequences were not available. Therefore, in this study, we performed the whole genome sequencing using Illumina short-read technology to construct draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur, of which Vechur is known as the smallest cow of the world. We also report the first de novo genome assemblies of these native B. indicus breeds. Further, we constructed the 18S rRNA marker gene sequences of these B. indicus breeds, which were not yet known. Genomic analysis helped to identify the distinct bovine phenotypic characteristics-related and other biological process-related genes in this species compared to B. taurus, and to gain comparative genomic insights between the dwarf and non-dwarf breeds of this species.

Ficus benghalensis (Indian banyan tree) and Ficus religiosa (Peepal) trees are well-known for their long lifespan, traditional significance, and medicinal properties. Therefore, to understand the genomic and evolutionary aspect of these characteristics the whole genomes of these two Ficus species were sequenced using 10x Genomics and Oxford Nanopore sequencing platforms. The draft genome assemblies of F. benghalensis (392.89 Mbp genome containing 25,016 high-confidence coding genes), and F. religiosa (332.97 Mbp genome containing 23,929 high-confidence coding genes) were constructed. We also established the genome-wide phylogenetic position of the two Ficus trees with respect to 46 other Angiosperm plant species and studied the comparative population demographic history of these two species to show a population bottleneck event ~0.8 Mya for both the species. We also identified 7,468 orthogroups across 16 phylogenetically closer Eudicot plant species including F. benghalensis and F. religiosa. Comparative evolutionary analyses using these orthogroups, gene family expansion/contraction analysis, and gene duplication analysis showed adaptive evolution in genes involved in cellular pathways and mechanisms that are central to plant growth and development and provide genomic insights into longevity and ecological significance of these large woody trees.

Phyllanthus emblica or Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position of P. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.