Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Closing Gaps in the Genome of the Fire Ant Solenopsis invicta

隨著新的定序技術的快速發展和定序成本的減少，基因體的研究現在可以應用到曾經不具有的參考基因體的非模型生物。最近發表的入侵紅火蟻紅火蟻的基因體是應用了次世代（Next Generation Sequencing）來定序一個對經濟和生態重要的非模式物種。然而，定序和裝配技術的局限性對於基因體的完整組裝造成了一些困難。這些新組裝的基因組被認為是基因體初稿，因為它們的片段基因序列內和之間含有未定序的間隙 （gaps）。因此，本論文旨在使用PCR、克隆和Sanger定序技術，以解決部分紅火蟻基因組體裡Linkage Group 16（LG16）的間隙。 LG 16，或 LG S（“social”）是有牽連到火蟻的社會行為的基因控制的重要染色體，本論文針對279缺口在染色體的特殊非重組區域 ( non-recombining supergene region)嘗試解析。而較大的間隙則透過跨越BAC克隆封閉。試驗結果顯示，在supergene區域的重複元素比此區域外的高10％。此現象可支持關於在非重組的區域容易造成有害元素累積的假說。透過這些解析的間隙序列不僅可以有利於一個更完整的基因體的組裝，而且還可以有助於揭示重要的基因組特徵，例如，在社會型染色體(social chromosome)裡的重複序列的瞭解。With the rapid development of new sequencing technologies and the drastic reduction to sequencing costs, genome wide sequencing studies can now be applied to non-model organisms that do not have established reference genomes. The recent publication of the genome of the invasive fire ant Solenopsis invicta is a good example of how such new advances in next generation sequencing technologies can be readily adopted for an economically and ecologically important non-model species. Nevertheless, limitations of the sequencing and assembly technologies create difficulties in achieving complete coverage of the entire genome. These newly assembled genomes are considered draft genomes, because they contain many gaps of unknown bases within and in between scaffolds. This project aims to resolve some of these gaps on linkage group 16 (LG 16) of the S. invicta draft genome by using a combination of PCR, cloning, and Sanger sequencing techniques. LG 16, or LG S (“social”), corresponds to a chromosome implicated to have important roles in the genetic control of the fire ant’s social behavior. A total of 279 gap closures were attempted inside and outside a special non-recombining region on LG 16. While larger inter-scaffold gaps were closed by screening for BAC clones that span across scaffolds. Sequencing results revealed a 10% higher proportion of repetitive elements inside the supergene than that of outside. These patterns are consistent with assembly biases which might support previous predictions regarding the accumulation of deleterious elements in the non-recombining region. These resolved gap sequences, in combination with BAC sequences that span inter-scaffold gaps would not only allow for the assembly of a more complete genome, but may also contribute to revealing important genomic features such as repetitive elements and genomic repeats in the social chromosome.Table of Contents Thesis Defense Completion Form ………………………………………………… i Acknowledgements ……………………………………………………………… ii Chinese Abstract ………………………………………………………………… iii Abstract …………………………………………………………………………… iv Table of Contents ………………………………………………………………… vi List of Figures …………………………………………………………………… viii List of Tables …………………………………………………………………… ix Introduction Next (Now) Generation Sequencing ……………………………………… 1 The Fire Ant Genome …………………………………………………… 2 Genetic Control of Social Structure …………………………………… 4 Gaps in the Social Chromosome …………………………………… 6 Materials and Methods General Strategy ………………………………………………………… 9 Gap Isolation ………………………………………………………………… 10 Primer Design …………………………………………………………… 10 PCR ………………………………………………………………………… 11 Cloning ……………………………………………………………………… 12 BAC Clones ………………………………………………………………… 12 Sequence Alignment ………………………………………………………… 13 Gap Reintegration …………………………………………………………… 14 Results Gap Resolution ……………………………………………………………… 15 Gap Closure Efficacy ……………………………………………………… 16 Gap Prediction …………………………………………………………… 17 Gap Categories ……………………………………………………………… 18 BAC Results ………………………………………………………………… 19 Gap Sizes …………………………………………………………………… 19 Non-repetitive Gaps ………………………………………………………… 20 Gap Reintegration …………………………………………………………… 20 Discussion Repetitive Elements ………………………………………………………… 21 Sequence/Assembly Bias …………………………………………………… 22 Conclusion ………………………………………………………………… 25 References ……………………………………………………………………… 27 Appendix I Gap Primer Pairs …………………………………………………… 44 Appendix II Gap Identities …………………………………………………… 6