Genome Assemblies, Analyses, and Comparisons

DNA测序技术的进步使基因组研究的新领域成为可能，使基因组变异和表型之间有了很好的联系。我们正在研究各种真核和原核非模式生物的转录本和基因组，并为获得生物学见解做出了贡献。目前，我们正在与哥伦比亚科波伊卡的研究人员合作，继续利用下一代测序技术产生的更多数据来表征海角猕猴桃转录组，并计划使用NCBI工具构建一个数据库，以显示新组装的海角猕猴桃转录组。此外，我们正在使用NCBIS原核基因组注释管道对来自哥伦比亚的本地肠炎沙门氏菌分离株进行组装和注释。这是与里查·阿加瓦拉和罗伯托·维拉·阿尔瓦雷斯合作完成的。 我们与John Spouge和Sergey Sheetlin合作，使用推广的Ruzzo-Tompa算法来寻找基因组序列中的重复序列，并实现了称为RepWords的算法，该实现允许惩罚删除不利字母，因此算法的推广包括缺口。程序RepWords在DNA中发现不精确的简单重复，通过比之前描述的类似特别工具更好地例证了一般概念。在另一项与I.King Jordan合作研究基因组中重复序列的研究中，我们测试了哺乳动物范围的散布重复序列(MIR)为人类基因组贡献功能增强剂的可能性。我们发现MIR高度集中在K562和HeLa人类细胞类型的增强子中，并且MIR衍生的增强子被发现是转录因子结合位点的丰富来源。因此，MIR可以在人类基因组中发挥调节功能，这项研究有助于解释为什么它们是最古老的转座元件家族。 我们为从临床和环境来源获得的三株海军弧菌的第一批基因组序列的组装和注释做出了贡献。使用太平洋生物科学和Illumina技术构建杂交组装，并使用NCBI原核基因组自动注释管道(PGAAP)对基因组进行注释。这项研究是与I·金·乔丹和谢丽尔·塔尔(CDC)合作完成的。在与卡洛斯·Y·索托合作的另一项研究中，我们发现了在共生分枝杆菌中合成糖肽类脂的新基因，有助于理解这些分枝杆菌中滑动运动、生物膜的形成和糖肽类脂的产生。

Technological advances in DNA sequencing are enabling new areas of genomic research allowing fine connections between genomic variants and phenotype. We are studying transcriptomes and genomes from a variety of eukaryotic and prokaryotic non model organisms and have contributed to gain biological insights. At the moment we are collaborating with researchers in Corpoica, Colombia to continue the characterization of the Cape gooseberry transcriptome with additional data generated by next-generation sequencing technologies and have plans to construct a database using NCBI tools to display the newly assembled Cape gooseberry transcriptome. Additionally, we are in the process of assembling and annotating native Salmonella enterica isolates from Colombia using the NCBIs Prokaryotic Genomes Annotation Pipeline. This is done in collaboration with Richa Agarwala and Roberto Vera Alvarez. In collaboration with John Spouge and Sergey Sheetlin, we have used the generalized Ruzzo-Tompa algorithm to find repeats in genomic sequences and made an implementation of the algorithm called RepWords, the implementation allows the penalized deletion of unfavorable letters, the algorithmic generalization therefore includes gaps. The program RepWords, which finds inexact simple repeats in DNA, exemplifies the general concepts by out-performing similar ad hoc previously described tools. In another study related to the investigation of repeated sequences in genomes in collaboration with I. King Jordan we tested the possibility that mammalian-wide interspersed repeats (MIRs) contribute functional enhancers to the human genome. We found that MIRs are highly concentrated in enhancers of the K562 and HeLa human cell-types and MIR-derived enhancers were found to be a rich source of transcription factor binding sites. Therefore, MIRs can exercise a regulatory function in the human genome and this study contributes to explain why their role as the most ancient family of transposable elements. We contributed to the genome assembly and annotation of the first genome sequences of three Vibrio navarrensis strains obtained from clinical and environmental sources. Hybrid assembly were constructed using Pacific Biosciences and Illumina technologies and the genomes were annotated with the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP). This research was done in collaboration with I. King Jordan and Cheryl Tarr (CDC). In a different study in collaboration with Carlos Y. Soto we identified novel genes for glycopeptidolipids biosynthesis in Mycobacterium colombiense, contributing to the understanding of sliding motility, biofilm formation, and glycopeptidolipid production in these mycobacteria.