Molecular characterization of TFE3-rearranged renal cell carcinoma in children and adolescents.

TFE3-rearranged renal cell carcinoma (TFE3-RCC) is a rare but aggressive subtype of kidney cancer that mainly affects young patients. However, the molecular characteristics of TFE3-RCCs in children and adolescents remain poorly understood. To this end, we performed a comprehensive study to characterize the genomic and transcriptional profiles of pediatric/adolescent TFE3-RCCs and compare them with those of adult tumors.

Preferential gene retention increases the robustness of cold regulation in and other plants after polyploidization.

Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three species and 17 other representative species, we found that both cold-related genes () and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms.

Recursive Paleohexaploidization Shaped the Durian Genome.

The durian () genome has recently become available, and analysis of this genome reveals two paleopolyploidization events previously inferred as shared with cotton ( spp.). Here, we reanalyzed the durian genome in comparison with other well-characterized genomes.

An Overlooked Paleotetraploidization in Cucurbitaceae.

Cucurbitaceae plants are of considerable biological and economic importance, and genomes of cucumber, watermelon, and melon have been sequenced. However, a comparative genomics exploration of their genome structures and evolution has not been available. Here, we aimed at performing a hierarchical inference of genomic homology resulted from recursive paleopolyploidizations.

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform.

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales.

Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants.

As a model plant to study perennial trees in the Salicaceae family, the poplar () genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape () genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation.

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.

Mainly due to their economic importance, genomes of 10 legumes, including soybean (), wild peanut ( and ), and barrel medic (), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape () and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations.

Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses.

Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses.