Eleutheronema tetradactylum Hi-C, HiFi, RNA and survey sequencing data

The muscle tissue collected from the E. tetradactylum was used for SMRT (Single Molecule, Real-Time) sequencing and Hi-C sequencing to employ genome assembly. For SMRT sequencing, the genomic libraries with insert 20 kb size were constructed and then sequenced on PacBio Sequel II platform in CCS mode. The raw data generated from PacBio Sequel II platform was filtered into high-precision HiFi reads.For Hi-C sequencing, we followed the formerly reported method18 to construct library. Muscle tissue ground from liquid nitrogen was cross-linked with formaldehyde and then cut with restriction enzyme. After labelling the enzyme-digested product by biotin, we connected it with cross-linked fragments. Subsequently, the SDS and proteinase K were used to reverse crosslinks and the magnetic bead was used to purify DNA. The purified DNA was then sheared to a length of 500bp to construct paired-end libraries and then sequenced on DNBSEQ platform.Eye, brain, liver, heart, spleen, kidney, muscle, and gill tissues of the E. tetradactylum from liquid nitrogen were used for transcriptome sequencing d on MGISEQ 2000 platform.The raw reads generated from the DNBSEQ platform were quality-filtered using fastp Jellyfsh was employed to calculate the Kmer frequency for the quality-filtered reads. GenomeScope2.0 was based on the Kmer frequency to estimate the genome size, heterozygosity, and repeat rate of E.tetradactylum.

本研究采集的四指马鲅（E. tetradactylum）肌肉组织用于单分子实时测序（Single Molecule, Real-Time, SMRT）及Hi-C测序，以开展基因组组装。针对单分子实时测序，我们构建了插入片段长度为20 kb的基因组文库，随后在PacBio Sequel II平台以CCS模式完成测序，其产出的原始数据经过滤后得到高精度HiFi reads。
Hi-C测序方面，我们参考已发表的方法18构建文库。将液氮研磨后的肌肉组织用甲醛进行交联，随后用限制性内切酶酶切；以生物素标记酶切产物后，将其与交联片段进行连接。随后使用SDS与蛋白酶K逆转交联反应，并利用磁珠纯化DNA。将纯化后的DNA剪切至500 bp长度以构建双端测序文库，随后在DNBSEQ平台完成测序。
本研究使用液氮保存的四指马鲅眼、脑、肝、心、脾、肾、肌肉及鳃组织开展转录组测序，测序平台为MGISEQ 2000。
DNBSEQ平台产出的原始reads使用fastp进行质量过滤，随后利用Jellyfish计算过滤后reads的Kmer频率。
基于上述Kmer频率，使用GenomeScope2.0评估四指马鲅的基因组大小、杂合率及重复序列比例。