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Salix suchowensis is a kind of shrub willow that blooms in the same year. It has the characteristics of fast-growing and high-yield, short rotation period, small individual, easy to reproduce and so on. It is an important biomass energy and afforestation timber tree species. Shrub willow is widely distributed, can adapt to different ecological environment, and has rich natural variation. It is an ideal material for studying forest genetic breeding. In July 2014, Professor Yin Tongming's research group of Nanjing Forestry University completed the second generation sequencing and assembly of the genome of Salix, which laid an important foundation for accelerating the research of molecular breeding of Salicaceae.
In April 2020, Professor Yin Tongming's research group of Nanjing Forestry University published a research paper entitled "the chrome scale assembly of the willow genome provides insight into salinaceae genome evolution" in horticulture research. In this study, a high-quality chromosome version of the reference genome of bojiliu was obtained by using three generations of pacbio sequencing and Hi-C technology. The newly assembled genome is 356 MB in size, and contig N50 is 263908 BP, 65 times larger than that of the previous version. 36937 protein coding genes have been annotated, and 95.29% of the genome sequence can be attached to 19 chromosomes. The newly assembled Salix psammophila has higher continuity and integrity, which will contribute to the comparative genomic research of Salicaceae species and provide high quality genomic resources for woody plant research. Fig. 1 Chromosomal features of Salix suchowensis.
Populus and Salix are sister genera of Salicaceae. Through comparative genomic analysis of Salix, it is found that both poplar and willow originated from the same ancestor and experienced the "salicoid" genome-wide replication event in Salicaceae. The 4 DTV mutation rate of the direct homology gene and the side homology gene of poplar and willow indicated that the genome differentiation of poplar and willow occurred after the "salicoid" genome replication event. The collinearity analysis between the chromosomes of poplar and willow further confirmed that the fission and fusion of chromosomes after "salicoid" replication event led to the differentiation of sister genera of Salix. Different Ka / Ks mutation rates in willow genome indicate that willow genome is under more pressure of purification and selection, which may be an important factor that makes the number of willow genes smaller than that of poplar. Fig.2 Four-fold synonymous third-codon transversion (4DTV) and the number of synonymous substitutions per synonymous site (Ks) for each homologous gene pair in S. suchowensis genome v2.0 and P. trichocarpa genome v3.0.
Fig.3 Syntenic comparison of the homologous chromosomes between S. suchowensis genome v2.0 and P. trichocarpa genome v3.0.
Fig.4 boxplot of Ka / Ks values for the parallel genes that area from salioid duplication on each chromosome in S. suchowensis and P. tricocarpa. Dr. Wei Suyun from the Key Laboratory of forest genetic breeding and variety improvement of Nanjing Forestry University is the first author of this paper, and Professor Yin Tongming is the corresponding author. This research is supported by the national key research and development plan (2016yfd060101).
Article link:
https://www.nature.com/articles/s41438-020-0268-6
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About Horticulture Research
Horticulture research is an English journal jointly founded by Nanjing Agricultural University and Nature Publishing Group (now Springer nature), which is the only special issue in the field of horticulture under nature. All basic and theoretical research on horticultural crops can be contributed. The influencing factors of horticulture research, Kerui Wei'an jcr2018 are 3.640, which are located in the first horticultural area (the 3rd / 36th) and the first plant science area (the 32nd / 228Th). Journal division of Chinese Academy of Sciences in 2019 (Basic Edition): it is located in the first area of horticulture, the first area of plant science and the first area of agriculture and Forestry Science (top journal).
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