Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1101/gr.213660.116 |
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set | |
Damas, Joana1; O’Connor, Rebecca2; Farre, Marta1; Lenis, Vasileios Panagiotis E.3; Martell, Henry J.2; Mandawala, Anjali2,4; Fowler, Katie4; Joseph, Sunitha2; Swain, Martin T.3; Griffin, Darren K.2; Larkin, Denis M.1 | |
通讯作者 | Larkin, Denis M. |
来源期刊 | GENOME RESEARCH |
ISSN | 1088-9051 |
EISSN | 1549-5469 |
出版年 | 2017 |
卷号 | 27期号:5页码:875-884 |
英文摘要 | Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome. |
类型 | Article |
语种 | 英语 |
国家 | England ; Wales |
收录类别 | SCI-E |
WOS记录号 | WOS:000400392400021 |
WOS关键词 | MOLECULAR CYTOGENETICS ; DNA-SEQUENCES ; AVIAN GENOME ; ROCK PIGEON ; EVOLUTION ; BIRDS ; CHICKEN ; INSIGHTS ; MAMMALS ; CATTLE |
WOS类目 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity |
WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity |
来源机构 | University of London |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/199162 |
作者单位 | 1.Univ London, Royal Vet Coll, Dept Comparat Biomed Sci, London NW1 0TU, England; 2.Univ Kent, Sch Biosci, Canterbury CT2 7NY, Kent, England; 3.Aberystwyth Univ, Isnt Biol Environm & Rural Sci, Aberystwyth SY23 3DA, Dyfed, Wales; 4.Canterbury Christ Church Univ, Sch Human & Life Sci, Canterbury CT1 1QU, Kent, England |
推荐引用方式 GB/T 7714 | Damas, Joana,O’Connor, Rebecca,Farre, Marta,et al. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set[J]. University of London,2017,27(5):875-884. |
APA | Damas, Joana.,O’Connor, Rebecca.,Farre, Marta.,Lenis, Vasileios Panagiotis E..,Martell, Henry J..,...&Larkin, Denis M..(2017).Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.GENOME RESEARCH,27(5),875-884. |
MLA | Damas, Joana,et al."Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set".GENOME RESEARCH 27.5(2017):875-884. |
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