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IDs: 14691991 [UID] 38034528 [GenBank] 42537698 [RefSeq]
The assembly ddMerAnnu1.2 is based on 58x PacBio data, 10X Genomics Chromium data, and Arima2 Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation ... with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with YaHS. The mitochondrial and chloroplast genomes were assembled using MBG from PacBio HiFi reads mapping to related genomes. A representative circular sequence was selected for each from the graph based on read coverage. Finally, the primary assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds are named by synteny based on PMID:31113811. Chromosome assignment for this assembly has been based on the genetic map produced by Veltsos P et al. Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics. 2019 Jul;212(3):815-835. PMID: 31113811. Owing to the sex chromosomes being homomorphic and recombining over an extensive autosomal region they were identified as a single linkage group. Therefore for this diploid female specimen X has been assigned LG1-X. more
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