Chlorella sp. MEM25 isolate:saltwater Genome sequencing
The dynamic adaptation of green algae from saltwater to freshwater is a complex evolutionary process that showcases the diversity of selective pressures from marine and freshwater environments. Both saltwater and freshwater species have independently evolved or inherited various adaptive mechanisms from their predecessors. MEM25 acts as a transitional point crossing over the salinity barrier, demonstrating dual environmental adaptation mechanisms. The genetic products of ancestral genes and lineage-specific genes collaboratively sculpt the adaptation of MEM25 to salinity changes. MEM25 possesses general modules related to salinity that are shared among freshwater Chlorophyta species (potentially extending to all green plants), alongside distinctive modules acquired through HGTs or other yet undiscovered mechanisms (e.g., orphan genes). Here, we have made public the complete genomic information of Chlorella sp.MEM25 to facilitate its more in-depth research and communication.Genome assembly details of MEM25: Single molecule real time sequencing (SMRT) libraries and Illumina short read libraries were constructed using fresh mid-log phase algae (BioMarker, China), followed by sequencing with the PacBio Sequel II and HiSeq 2000 platforms. The Hi-C library and sequencing were conducted with the Illumina HiSeq platform (Novogene, China). Multiple approaches have been employed to guarantee the quality of genome sequences. PacBio and Hi-C data, Hifiasm (version 0.16.1-r375) was used for subgenome splitting. SMRT sequencing data were assembled using Falcon (version 0.3.0) and CANU (version 2.1.1). 3D-DNA (version 180922) and ALLHiC (version 0.9.8) were used for draft genome correction and genome assembly, respectively. Finally, Juicebox (version 1.11.08) and Pilon (version 1.24) were used to correct genome fragments (based on the chromosome contact frequency matrix) and base errors of the genome with Illumina and RNA-seq data, respectively. The Hi-C interaction frequency matrix was analyzed by Homer, FitHic (version 2.0.8), HiCExplorer (version 3.7.2), and HiCCUPS (version 5.14). The 3-D chromosome coordinate location was calculated using HiC-GNN and was visualized using UCSF Chimera (version 1.15).