Kmasker plants - a tool for assessing complex sequence space in plant species

被引：6

作者：

Beier, Sebastian ^{[1
]}

Ulpinnis, Chris ^{[2
]}

Schwalbe, Markus ^{[1
]}

Muench, Thomas ^{[1
]}

Hoffie, Robert ^{[1
]}

Koeppel, Iris ^{[1
]}

Hertig, Christian ^{[1
]}

Budhagatapalli, Nagaveni ^{[1
]}

Hiekel, Stefan ^{[1
]}

Pathi, Krishna M. ^{[1
]}

Hensel, Goetz ^{[1
]}

Grosse, Martin ^{[1
,4
]}

Chamas, Sindy ^{[1
,5
]}

Gerasimova, Sophia ^{[1
,6
]}

Kumlehn, Jochen ^{[1
]}

Scholz, Uwe ^{[1
]}

Schmutzer, Thomas ^{[3
]}

机构：

[1] Leibniz Inst Plant Genet & Crop Plant Res IPK Gat, D-06466 Seeland, Germany

[2] Leibniz Inst Plant Biochem Bioinformat & Sci Data, D-06120 Halle, Germany

[3] Martin Luther Univ Halle Wittenberg, Inst Agr & Nutr Sci, Dept Nat Sci 3, D-06120 Halle, Germany

[4] Univ Lubeck, Inst Cardiogenet, D-23562 Lubeck, Germany

[5] Erfurt Univ Appl Sci, Erfurt Res Ctr Hort Crops, D-99090 Erfurt, Germany

[6] RAS, SB, Inst Cytol & Genet, Novosibirsk 630090, Russia

来源：

PLANT JOURNAL | 2020年 / 102卷 / 03期

关键词：

comparative genomics; sequence analysis; plant genomics; k-mer analysis; repeat masking; CRISPR; genome editing; technical advance; K-MER; SECALE-CEREALE; GUIDE RNA; CRISPR-P; SOFTWARE; CHROMOSOMES; QUALITY; HORDEUM; DESIGN; PROBES;

D O I：

10.1111/tpj.14645

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Many plant genomes display high levels of repetitive sequences. The assembly of these complex genomes using short high-throughput sequence reads is still a challenging task. Underestimation or disregard of repeat complexity in these datasets can easily misguide downstream analysis. Detection of repetitive regions by k-mer counting methods has proved to be reliable. Easy-to-use applications utilizing k-mer counting are in high demand, especially in the domain of plants. We present Kmasker plants, a tool that uses k-mer count information as an assistant throughout the analytical workflow of genome data that is provided as a command-line and web-based solution. Beside its core competence to screen and mask repetitive sequences, we have integrated features that enable comparative studies between different cultivars or closely related species and methods that estimate target specificity of guide RNAs for application of site-directed mutagenesis using Cas9 endonuclease. In addition, we have set up a web service for Kmasker plants that maintains pre-computed indices for 10 of the economically most important cultivated plants. Source code for Kmasker plants has been made publically available at . The web service is accessible at .

引用

页码：631 / 642

页数：12

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