“…Among all the core Eudicot species in our phylogenetic tree, the species from the Saxifragales plant order (K. fedtschenkoi) diverged the earliest. The relative phylogenetic positions of the Eudicot orders were similar to the previous studies (Soltis et al, 2000;Chakraborty et al, 2022).…”
Section: Collinearity and Orthologous Gene Clusteringsupporting
Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world’s largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.
“…Among all the core Eudicot species in our phylogenetic tree, the species from the Saxifragales plant order (K. fedtschenkoi) diverged the earliest. The relative phylogenetic positions of the Eudicot orders were similar to the previous studies (Soltis et al, 2000;Chakraborty et al, 2022).…”
Section: Collinearity and Orthologous Gene Clusteringsupporting
Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world’s largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.
“…1A ; Figure S2 ; Table 1 ). The contig N50 was 19.71 Mb, which has higher integrity and continuity (contigs N50: 0.18 to 2.29 Mb) (Table S2 ), compared to F. carica (8.23 Mb) 28 , F. microcarpa (1.77 Mb) 29 , F. hispida (2.16 Mb) 29 , and F. religiosa (5.53 Mb) 30 . Fig.…”
Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus.
“…This result was further used for training AUGUSTUS v3.2.3 gene prediction program [51] for our species and SNAP v2006-07-28 gene prediction program, and the training results were used for a third round of MAKER annotation [52]. After the third or final round of MAKER annotation, coding genes were filtered based on AED (Annotation Edit Distance) value <0.5, and length of ≥ 150 bases to construct the final high-confidence coding gene set of blue peafowl [53]. Additionally, the high-quality genome assembly of blue peafowl was also used for de novo prediction of tRNAs and rRNAs using tRNAscan-SE v2.0.7 [54] and Barrnap v0.9 (https://github.com/tseemann/barrnap), respectively, and for homology-based identification of miRNAs using MirGeneDB v2.1 database [55] using BLASTN (95% query coverage and 95% sequence identity).…”
An intriguing example of differential adaptability is the case of two Asian peafowl species,Pavo cristatus(blue peafowl) andPavo muticus(green peafowl), where the former has a ″Least Concern″ conservation status and the latter is an ″Endangered″ species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of unique gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly ofP. cristatusconstructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.
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