PLANT BIOTECHNOLOGY JOURNAL

Plant Biotechnology Journal

Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome

Navrátilová P., Toegelová H., Tulpová Z., Kuo Y.-T., Stein N., Doležel J., Houben A., Šimková H., Mascher M.
PLANT BIOTECHNOLOGY JOURNAL 20 : 1373-1386 , 2022
Keywords: PacBio HiFi reads, nanopore, flow cytometry, ChIP-seq, CenH3, Cereba, telomeric repeats, satellite, ribosomal DNA

Long-range assembly of sequences helps to unravel the genome structure and small variation of the wheat–Haynaldia villosa translocated chromosome 6VS.6AL

Xing L., Yuan L., Lv Z., Wang Q., Yin Ch., Huang Z., Liu J., Cao S., Zhang R., Chen P., Karafiátová M., Vrána J., Bartoš J., Doležel J., Cao A.
PLANT BIOTECHNOLOGY JOURNAL 19 : 1567-1578 , 2021
Keywords: wheat–Haynaldia villosa translocation line T6VS.6AL, Chicago long-range linkage assembly, genome annotation, InDel markers, physical bin map

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Feng, K., Cui, L., Wang, L., Shan, D., Tong, W., Deng, P., Yan, Z., Wang, M., Zhan, H., Wu, X., He, W., Zhou, X., Ji, J., Zhang, G., Mao, L., Karafiátová, M., Šimková, H., Doležel, J., Du, X., Zhao, S., Luo, M.C., Han, D., Zhang, C., Kang, Z., Appels, R., Edwards, D., Nie, X., Weining, S.
PLANT BIOTECHNOLOGY JOURNAL 18 : 732-742 , 2020
Keywords: 7DL chromosome arm; BAC by BAC; domestication; gene loss; physical mapping; wheat

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Akpinar, B. A., Biyiklioglu, S., Alptekin, B., Havránková, M., Vrána, J., Doležel, J., Distelfeld, A., Hernandez, P., The IWGSC, Budak, H.
PLANT BIOTECHNOLOGY JOURNAL 16 : 2077-2087 , 2018
Keywords: wild emmer wheat, chromosome sorting, hexaploid wheat, next-generation sequencing, comparative genomics.

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat

Rey, E., Abrouk, M., Keeble-Gagnère, G., Karafiátová, M., Vrána, J., Balzergue, S., Soubigou-Taconnat, L., Brunaud, V., Martin-Magniette, M.L., Endo, T.R., Bartoš, J.; International Wheat Genome Sequencing Consortium (IWGSC), Appels, R., Doležel, J.
PLANT BIOTECHNOLOGY JOURNAL 16 : 1767-1777 , 2018
Keywords: alien introgression, RNAseq, gene transcription, transcriptome modification, chromosomal rearrangement, deletion

An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance

Kaur P., Bayer P.E., Milec Z., Vrána J., Yuan Y., Appels R., Edwards D., Batley J., Nichols P., Erskine W., Doležel J.
PLANT BIOTECHNOLOGY JOURNAL 15 : 1034-1046 , 2017
Keywords: forage legumes, advanced reference assembly, BioNano, transcriptome, gene expression, Legume comparative genomics

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

Abrouk, M., Balcárková, B., Šimková, H., Komínkova, E., Martis, M.M., Jakobson, I., Timofejeva, L., Rey, E., Vrána, J., Kilian, A., Järve, K., Doležel, J., Valárik, M.
PLANT BIOTECHNOLOGY JOURNAL 15 : 249-256 , 2017
Keywords: GenomeZipper, alien introgression, comparative analysis, chromosome rearrangement, chromosome translocation, linkage drag

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Staňková, H., Hastie, A.R., Chan, S., Vrána, J., Tulpová, Z., Kubaláková, M., Visendi, P., Hayashi, S., Luo, M., Batley, J., Edwards, D., Doležel, J., Šimková, H.
PLANT BIOTECHNOLOGY JOURNAL 14 : 1523-1531 , 2016
Keywords: optical mapping, wheat, sequencing, physical map, flow sorting, chromosomes

Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)

Akpinar, B.A., Lucas, S.J., Vrána, J., Doležel, J., Budak, H.
PLANT BIOTECHNOLOGY JOURNAL 13 : 740-752 , 2015
Keywords: D genome donor of wheat, chromosome 5D, comparative genomics

A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

Ruperao, P., Chan, C.K., Azam, S., Karafiátová, M., Hayashi, S., Cížková, J., Saxena, R.K., Šimková, H., Song, C., Vrána, J., Chitikineni, A., Visendi, P., Gaur, P.M., Millán, T., Singh, K.B., Taran, B., Wang, J., Batley, J., Doležel, J., Varshney, R.K., Edwards, D.
PLANT BIOTECHNOLOGY JOURNAL 12 : 778-786 , 2014
Keywords: chickpea, genome assembly, cytogenetics, cicer