Gemy Kaithakottil

This paper presents a chromosome-scale genome of Thinopyrum bessarabicum, showing the J genome is not part of polyploid Thinopyrum ancestry and identifies genomic features linked to salt tolerance.

This study uses spatial transcriptomics to analyze gene expression gradients in wheat inflorescences, revealing dynamic spatio-temporal organization along the apical-basal axis.

The paper presents a high-quality genome assembly for the GIANT Nile tilapia strain, enabling the reconstruction of X and Y haplotypes and identifying sex determination loci on LG23.

This study identifies C16-hydroxylated triterpenoids as key anti-inflammatory compounds in Calendula officinalis and reconstructs their biosynthetic pathway for production.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

The paper presents a reference genome assembly for the Violet Carpenter Bee, including gene annotation and mitochondrial genome, as part of the European Reference Genome Atlas.

This study annotates the wheat pan-transcriptome de novo and identifies gene diversity and expression patterns across multiple wheat cultivars and tissues.

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

The paper presents a chromosome-level genome assembly for the GIFT tilapia strain, identifying introgressed regions from O. mossambicus associated with growth and immunity traits.

The paper presents a chromosome-scale rye genome assembly to study genomic evolution and agronomic traits in Triticeae crops.

Grass pea, a diploid legume with a 6.3 Gbp genome, gets two draft assemblies, one short-read and one Nanopore, plus 33,819 annotated genes.

The paper identifies an aphid gene family that translocates RNA into plants, promoting aphid reproduction and indicating cross-kingdom RNA deployment.

This study analyzes DNA methylation and gene expression differences between male and asexual female morphs of the green peach aphid, finding sex-specific methylation patterns linked to sexual differentiation.

Portcullis filters false splice junctions from RNA-seq alignments with high accuracy and efficiency, scaling well for large datasets and fragmented genomes.

The paper presents an algorithm to improve transcript annotation by integrating multiple RNA-Seq assemblies and introduces an open-source tool for this purpose.

The paper analyzes the genetic diversity of Hymenoscyphus fraxineus, showing the European population was founded by two divergent haplotypes with adaptive potential.

This study shows that the green peach aphid uses rapid transcriptional changes of duplicated genes to colonize diverse host plants without genetic specialization.