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Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

Identifikátory výsledku

  • Kód výsledku v IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F22%3A00566693" target="_blank" >RIV/61389030:_____/22:00566693 - isvavai.cz</a>

  • Výsledek na webu

    <a href="https://doi.org/10.1016/j.cj.2022.02.001" target="_blank" >https://doi.org/10.1016/j.cj.2022.02.001</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1016/j.cj.2022.02.001" target="_blank" >10.1016/j.cj.2022.02.001</a>

Alternativní jazyky

  • Jazyk výsledku

    angličtina

  • Název v původním jazyce

    Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

  • Popis výsledku v původním jazyce

    Erianthus arundinaceus is a wild relative of sugarcane (Saccharum officinarum L.) with many desirable agronomic traits for sugarcane genetic improvement. However, limited knowledge of the complex genome of hexaploid E. arundinaceus has impeded the development of required molecular tools. Dissecting complex genomes into single chromosomes can simplify analyses. The flow-cytometric sorting of a single chromosome of E. arundinaceus in a Saccharum–Erianthus introgression line is reported. A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size. A total of 218,000 E. arundinaceus chromosome 1 (EaC1) were sorted to >97% purity and amplified DNA was sequenced using Illumina and PacBio technologies. The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb. A total of 56.69 Mb repeat sequences were predicted, accounting for 79.1% of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59% of the chromosome. Of these genes, 1877 (70.9%) genes were functionally annotated. The phylogenetic relationship of E. arundinaceus with other species using the chromosome 1 sequence revealed that E. arundinaceus was distantly related to Oryza sativa and Zea mays, followed by Sorghum bicolor, and was closely related to S. spontaneum and Saccharum spp. hybrids. This study provides the first insights into the characteristics of EaC1, and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

  • Název v anglickém jazyce

    Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

  • Popis výsledku anglicky

    Erianthus arundinaceus is a wild relative of sugarcane (Saccharum officinarum L.) with many desirable agronomic traits for sugarcane genetic improvement. However, limited knowledge of the complex genome of hexaploid E. arundinaceus has impeded the development of required molecular tools. Dissecting complex genomes into single chromosomes can simplify analyses. The flow-cytometric sorting of a single chromosome of E. arundinaceus in a Saccharum–Erianthus introgression line is reported. A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size. A total of 218,000 E. arundinaceus chromosome 1 (EaC1) were sorted to >97% purity and amplified DNA was sequenced using Illumina and PacBio technologies. The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb. A total of 56.69 Mb repeat sequences were predicted, accounting for 79.1% of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59% of the chromosome. Of these genes, 1877 (70.9%) genes were functionally annotated. The phylogenetic relationship of E. arundinaceus with other species using the chromosome 1 sequence revealed that E. arundinaceus was distantly related to Oryza sativa and Zea mays, followed by Sorghum bicolor, and was closely related to S. spontaneum and Saccharum spp. hybrids. This study provides the first insights into the characteristics of EaC1, and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

Klasifikace

  • Druh

    J<sub>imp</sub> - Článek v periodiku v databázi Web of Science

  • CEP obor

  • OECD FORD obor

    10608 - Biochemistry and molecular biology

Návaznosti výsledku

  • Projekt

    <a href="/cs/project/EF16_019%2F0000827" target="_blank" >EF16_019/0000827: Rostliny jako prostředek udržitelného globálního rozvoje</a><br>

  • Návaznosti

    I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Ostatní

  • Rok uplatnění

    2022

  • Kód důvěrnosti údajů

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Údaje specifické pro druh výsledku

  • Název periodika

    Crop Journal

  • ISSN

    2095-5421

  • e-ISSN

    2214-5141

  • Svazek periodika

    10

  • Číslo periodika v rámci svazku

    6

  • Stát vydavatele periodika

    CN - Čínská lidová republika

  • Počet stran výsledku

    9

  • Strana od-do

    1746-1754

  • Kód UT WoS článku

    000901532600001

  • EID výsledku v databázi Scopus

    2-s2.0-85127365058