Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

作者:Wei Fusheng*; Stein Joshua C; Liang Chengzhi; Zhang Jianwei; Fulton Robert S; Baucom Regina S; De Paoli Emanuele; Zhou Shiguo; Yang Lixing; Han Yujun; Pasternak Shiran; Narechania Apurva; Zhang Lifang; Yeh Cheng Ting; Ying Kai; Nagel Dawn H; Collura Kristi; Kudrna David; Currie Jennifer; Lin Jinke; Kim HyeRan; Angelova Angelina; Scara Gabriel; Wissotski Marina; Golser Wolfgang; Courtney Laura; Kruchowski Scott; Graves Tina A; Rock Susan M; Adams Stephanie
来源:PLoS Genetics, 2009, 5(11): e1000728.
DOI:10.1371/journal.pgen.1000728

摘要

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e. g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on similar to 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

  • 出版日期2009-11