A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance

作者: Nathalie Pavy , Manuel Lamothe , Betty Pelgas , France Gagnon , Inanç Birol

DOI: 10.1111/TPJ.13478

关键词:

摘要: Over the last decade, extensive genetic and genomic resources have been developed for conifer white spruce (Picea glauca, Pinaceae), which has one of largest plant genomes (20 Gbp). Draft genome sequences other conifers recently produced, but dense maps are needed to comprehend macrostructure, delineate regions involved in quantitative traits, complement functional investigations, assist assembly fragmented sequences. A greatly expanded P. glauca composite linkage map was generated from a set 1976 full-sib progeny, with positioning 8793 expressed genes. Regions significant low or high gene density were identified. Gene family members tended be mapped on same chromosomes, tandemly arrayed genes significantly biased towards specific classes. The integrated transcriptome data surveyed across eight tissues. In total, 69 clusters co-expressed co-localising level synteny found pine maps, should facilitate transfer structural information Pinaceae. Although current sequence remains highly fragmented, dozens scaffolds encompassing more than From these, relationship between physical distances examined genome-wide recombination rate much smaller most estimates reported angiosperm genomes. This shall large-scale next-generation provide reference resource genomics community.

参考文章(77)
Marina de Miguel, Jérôme Bartholomé, François Ehrenmann, Florent Murat, Yoshinari Moriguchi, Kentaro Uchiyama, Saneyoshi Ueno, Yoshihiko Tsumura, Hélène Lagraulet, Nuria de Maria, José-Antonio Cabezas, Maria-Teresa Cervera, Jean Marc Gion, Jérôme Salse, Christophe Plomion, Evidence of intense chromosomal shuffling during conifer evolution. Genome Biology and Evolution. ,vol. 7, pp. 2799- 2809 ,(2015) , 10.1093/GBE/EVV185
L. Savard, P. Li, S. H. Strauss, M. W. Chase, M. Michaud, J. Bousquet, Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants Proceedings of the National Academy of Sciences of the United States of America. ,vol. 91, pp. 5163- 5167 ,(1994) , 10.1073/PNAS.91.11.5163
Brandon S. Gaut, Stephen I. Wright, Carène Rizzon, Jan Dvorak, Lorinda K. Anderson, Recombination: an underappreciated factor in the evolution of plant genomes Nature Reviews Genetics. ,vol. 8, pp. 77- 84 ,(2007) , 10.1038/NRG1970
Betty Pelgas, Stéphanie Beauseigle, Virginie Acheré, Sylvain Jeandroz, Jean Bousquet, Nathalie Isabel, Comparative genome mapping among Picea glauca, P. mariana × P. rubens and P. abies, and correspondence with other Pinaceae Theoretical and Applied Genetics. ,vol. 113, pp. 1371- 1393 ,(2006) , 10.1007/S00122-006-0354-7
Mehul S. Bhakta, Valerie A. Jones, C. Eduardo Vallejos, Punctuated Distribution of Recombination Hotspots and Demarcation of Pericentromeric Regions in Phaseolus vulgaris L. PLOS ONE. ,vol. 10, pp. e0116822- ,(2015) , 10.1371/JOURNAL.PONE.0116822
Carene Rizzon, Loic Ponger, Brandon S Gaut, Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLOS Computational Biology. ,vol. 2, ,(2005) , 10.1371/JOURNAL.PCBI.0020115