Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum

2021 ◽  
Author(s):  
Tao Lin ◽  
Xia Xu ◽  
Huilong Du ◽  
Xiuli Fan ◽  
Qingwen Chen ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Extensive Sequence ◽  
Reference Genomes

scholarly journals Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

2019 ◽  
Author(s):  
Raúl A. González-Pech ◽  
Yibi Chen ◽  
Timothy G. Stephens ◽  
Sarah Shah ◽  
Amin R. Mohamed ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Individual Species ◽  
Ecological Niches ◽  
Whole Genome ◽  
Structural Rearrangements ◽  
Extensive Sequence ◽  
Gene Functions

AbstractDinoflagellates of the family Symbiodiniaceae (Order Suessiales) are predominantly symbiotic, and many are known for their association with corals. The genetic and functional diversity among Symbiodiniaceae is well acknowledged, but the genome-wide sequence divergence among these lineages remains little known. Here, we present de novo genome assemblies of five isolates from the basal genus Symbiodinium, encompassing distinct ecological niches. Incorporating existing data from Symbiodiniaceae and other Suessiales (15 genome datasets in total), we investigated genome features that are common or unique to these Symbiodiniaceae, to genus Symbiodinium, and to the individual species S. microadriaticum and S. tridacnidorum. Our whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. We observed extensive structural rearrangements among symbiodiniacean genomes; those from two distinct Symbiodinium species share the most (853) syntenic gene blocks. Functions enriched in genes core to Symbiodiniaceae are also enriched in those core to Symbiodinium. Gene functions related to symbiosis and stress response exhibit similar relative abundance in all analysed genomes. Our results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This is the first comprehensive comparison of Symbiodiniaceae based on whole-genome sequence data, including comparisons at the intra-genus and intra-species levels.

scholarly journals Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

2016 ◽  
Vol 113 (35) ◽  
pp. E5163-E5171 ◽  
Author(s):  
Jianwei Zhang ◽  
Ling-Ling Chen ◽  
Feng Xing ◽  
David A. Kudrna ◽  
Wen Yao ◽  
...  
Keyword(s):  
Reference Genome ◽  
Indica Rice ◽  
Sequence Divergence ◽  
Segmental Duplications ◽  
Cultivated Rice ◽  
High Quality ◽  
Rice Varieties ◽  
The Public ◽  
Structural Differences ◽  
Reference Genomes

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059–2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

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