BMC GENOMICS

Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

Xiao, J., Dai, K., Fu, L., Vrána, J., Kubaláková, M., Wan, W., Sun, H., Zhao, J., Yu, C., Wu, Y., Abrouk, M., Wang, H., Doležel, J., Wang, X.
BMC GENOMICS 18 : 791 , 2017
Keywords: Haynaldia villosa, Flow sorting, Chromosome arm 4VS, Scaffold, Genome zipper

Identification of miRNAs with potential roles in regulation of anther development and male-sterility in 7B-1 male-sterile tomato mutant.

Omidvar V, Mohorianu I, Dalmay T, Fellner M
BMC GENOMICS 16 : 878- 893 , 2015
Keywords:

Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing

Wang, H., Dai, K., Xiao, J., Yuan, C., Zhao, R., Doležel, J., Wu, Y., Cao, A., Chen, P., Zhang, S., Wang, X.
BMC GENOMICS 18 : 167 , 2017
Keywords: Triticum aestivum, Haynaldia villosa, Molecular marker, Intron polymorphism

The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements

Evtushenko, E.V., Levitsky, V.G., Elisafenko, E.A., Gunbin, K.V., Belousov, A.I., Šafář, J., Doležel, J., Vershinin, A.V.
BMC GENOMICS 17 : 337 , 2016
Keywords: Tandem repeats, Transposable elements, Subtelomeric heterochromatin, Rye, Secale cereale, 1RS BAC library, 454 sequences, TE–tandem junctions, DNA motifs

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

Martin, G., Baurens, F.-C., Droc, G., Rouard, M., Cenci, A., Kilian, A., Hastie, A., Doležel, J., Aury, J.-M., Alberti, A., Carreel, F., D’Hont, A.
BMC GENOMICS 17 : 243 , 2016
Keywords: Musa acuminata, Genome assembly, Bioinformatics tool, Paired-end sequences, GBS, Genome map

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Blavet, N., Blavet, H., Muyle, A., Käfer, J., Cegan, R., Deschamps, C., Zemp, N., Mousset, S., Aubourg, S., Bergero, R., Charlesworth, D., Hobza, R., Widmer, A., Marais, G.A.B.
BMC GENOMICS 16 : 546 , 2015
Keywords: Sex chromosomes, Sex-linked genes, Plant, BAC, RNA-seq, Gene loss, Y degeneration, Silene latifolia, Silene vulgaris

High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

Wu Z.Q., Stone J.D., Štorchová H., Sloan D.B.
BMC GENOMICS 16 : 938 , 2015
Keywords: antisense RNA; junk DNA; mtDNA; ORFs; plant mitochondrial genome; regulatory RNA; spurious transcription

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

Kumar, A., Seetan, R., Mergoum, M., Tiwari, V.K., Iqbal, M.J., Wang, Y., Al-Azzam, O., Šimková, H., Luo, M.C., Dvorak, J., Gu, Y.Q., Denton, A., Kilian, A., Lazo, G.R., Kianian, S.F.
BMC GENOMICS 16 : 800 , 2015
Keywords: Aegilops tauschii, Deletion, Physical mapping, Radiation hybrid mapping, Sequence assembly, Wheat

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B

Kobayashi, F., Wu, J., Kanamori, H., Tanaka, T., Katagiri, S., Karasawa, W., Kaneko, S., Watanabe, S., Sakaguchi, T., Hanawa, Y., Fujisawa, H., Kurita, K., Abe, C., Iehisa, J.C.M., Ohno, R., Šafář, J., Šimková, H., Mukai, Y., Hamada, M., Saito, M., Ishikawa, G., Katayose, Y., Endo, T.R., Takumi, S., Nakamura, T., Sato, K., Ogihara, Y., Hayakawa, K., Doležel, J., Nasuda, S., Matsumoto, T., Handa, H.
BMC GENOMICS 16 : 595 , 2015
Keywords: Centromere, Chromosomal rearrangement, Chromosome 6B, DNA marker, Gene order, Nucleolus organizer region, BAC physical map, RH map, Synteny, Wheat

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

Akpinar, B.A., Magni, F., Yuce, M., Lucas, S.J., Šimková, H., Šafář, J., Vautrin, S., Bergès, H., Cattonaro, F., Doležel. J., Budak, H.
BMC GENOMICS 16 : 453 , 2015
Keywords: Triticum aestivum, 5DS, Hexaploid wheat, Physical mapping, Gene space, Grass evolution