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A high-quality chromosome-level genome scaffold is of paramount importance to drive innovation and new scientific knowledge for non-model organisms. However, chromosome-level scaffolding and accurate genome annotation from plant drafts is a notoriously difficult problem, especially when dealing with regions that overlap sections with many differences between haplotypes with homozygous regions. Although the use of modern algorithms, long reads, and complementary techniques such as Hi-C has greatly improved the overall accuracy and efficiency of assembly pipelines, this step remains a computationally challenging problem. A variety of techniques have been developed to solve the scaffolding problem, each with its own weaknesses and strengths, although using a combination of multiple scaffolding methods is generally better for generating chromosome-level assemblies than using a single approach. While understanding the genomic features of non-model organisms can be critical for new scientific discoveries, especially in the context of responses to stress conditions, the panorama of genome assemblies available for the Velloziaceae family is dismal. Only two publicly available genomes (one for Acanthochlamys bracteata and one for Xerophyta viscosa) are currently available to the scientific community. In this project, we scaffolded two draft genomes from different species of the genus Vellozia: Vellozia tubiflora and Vellozia peripherica. These endemic species of the Brazilian Campos Rupestres can thrive even under adverse environmental conditions, a phenotype achieved after millions of years of natural selection. By deciphering the genomic traits associated with response to various stresses, we can transfer the molecular basis of stress tolerance to other economically relevant plants. Considering that crops are among the most important commodities in Brazil, even small savings can have impacts on the order of millions of dollars per year. We not only performed a direct comparison of eight different scaffolding algorithms using reference-based and de novo strategies, but also evaluated the performance of hydride strategies using existing genome references and Hi-C data to generate high-quality chromosome-level. Our results show that by combining high-throughput experiments with the use of genomes already available in public databases, we were able to overcome the most common problems in genome assembly of novel organisms. By producing a high quality genome with structural and functional annotations, we are able to provide a solid foundation for any "omics" projects that might be undertaken by the scientific community interested in studying plant adaptation to various stresses.

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#	Name
1	Felipe Ciamponi(felipe.ciamponi@gmail.com,)
2	Mariana Cavalheiro(cavalheiromf@gmail.com)
3	Stephen Richards(stephenr@bcm.edu)
4	Harris Lewin(lewin@ucdavis.edu,)
5	Paulo Arruda(parruda@unicamp.br,)
6	Ricardo Dante(ricardo.dante@embrapa.br)
7	Isabel Gerhardt(isabel.gerhardt@embrapa.br)

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