| Collichthys lucidus,belongs to Perciformes,Sciaenidae,Collichthys,is mainly distributed in the shore waters of the northwestern Pacific,covering from the north of Australia to Sea of Japan with the pattern of north-south differentiation in China’s coastal.C.lucidus is a commercially important marine fish species,which is a potential aquaculture specie with development value and has been widely consumed in coastal regions in China.Previous research of us shows that C.lucidus is the only specie in Sciaenidae that has been found a multiple sex chromosome system with the X1X1X2X2/X1X2Y sex chromosome system.However,the scanty genetic basic research of C.lucidus is difficult to support the in-depth development of the biological research,resource conservation and application of the population.Therefore,this study resorts to Illumina,PacBio and Hi-C sequencing technology to construct chromosome-level assembly reference genome of C.lucidus with annotated to obtain gene structure information such as protein-coding genes,repeat sequences and non-coding RNA,and with the view to determining the phylogenetic status and the divergence time of the C.lucidus through evolutionary analysis.At the same time,a variety of methods were used to identify the X1 and X2 chromosomes respectively based on the repeat sequence characteristics of X1 chromosome which have been reported and the Hi-C interaction map.Furthermore,a preliminary study of the X1 chromosome repeat sequence is carried out.The main results of this study are as follows:(1)This study assembled a reference genome of C.lucidus on the chromosome-level with contigs N50 at 1.10 Mb as well as the scaffold N50 at 35.92 Mb,and acquired orderly and directional chromosomal sequences 0.84 Gb,representing 96.86%of the total assembled genome.A total of 304.4 Mb repeat sequence was annotated and accounted for 34.68%of the whole genome length,wherein 33.68%of the length of all repeat sequence was occupied by DNA transposons.A total of 28,032 protein-coding genes were annotated on function terms,including more than 97%of the BUSCO vertebrate and actinopterygii database genes.Moreover,1,608 rRNA sequences,7,655 tRNA sequences,1,595 miRNA sequences and 770 snRNA sequences were annotated.The C.lucidus genomic sequencing data were deposited in the Sequence Read Archive(https://www.ncbi.nlm.nih.gov/sra)at NCBI with SRA accession SRR8208332,SRR8142901,SRR8208331,SRR8208301,and the final chromosome assembly and annotation were deposited in the GenBank(ftp://ftp.ncbi.nlm.nih.gov/genomes)at NCBI SCMI00000000.1.(2)By the phylogenetic relationship analyze between the C.lucidus and other 11 representative fishes,there are 15,472 gene families in the C.lucidus,including 354 unique gene families.The number of total gene families and unique gene families(number of genes)rank the first among 12 species of fish.The results of expansion and contraction gene analysis showed that the expansion genes of the C.lucidus were mainly related to signal transduction,nervous system and immune system;while the contraction genes were mainly related to signal transduction,transmembrane transport;immune system and digestive system.It was estimated based on evolutionary analysis that the C.lucidus and the large yellow croaker which have the closest relationship differentiated about 43.4 million years ago.By the collinearity analysis,the genomes of the C.lucidus and the large yellow croaker kept a high level of collinearity,and the chromosomal variation mainly occurred at the inversion and translocation within the arms on several chromosomes,as well as interchromosomal translocation of two chromosomes.Furthermore,the repeat segment of chromosome 1 has no corresponding segment in the large yellow croaker genome.While the chromosome 1 of the C.lucidus and the zebrafish chromosome 4,which also has a repeat sequence aggregated,are not homologous chromosomes.(3)It is judged that chromosome 1 is the X1 chromosome through that repeated sequence of 5S rRNA,(CAT)n,(CAG)n.on chromosome 1 of the C.lucidus consistent with the molecular cytogenetic characteristics of the known X1 chromosome.The chromosome 7 was preliminary determined as the X2 chromosome for chromosome 7 showed strong interaction with chromosome 1 on the Hi-C interaction map of the male C.lucidus relative to the reference genome of female.(4)A lot of repeat sequence aggregated at the segment of approximately 23 Mb from the proximal end of chromosome 1,which is generally higher than 75%and much higher than the average content of the whole genome repeat(34.68%).Meanwhile,LTR and LINE in this segment accounted for 54.25%of the length of all repeats in the segment are much higher than the average rate of 2 to 24 chromosomes(12.42%).The results of this study provide a rich data source for basic biology research,resource conservation,genetic breeding and comparative genomics research of the C.lucidus,and lays a foundation for further analysis of the sex chromosome evolution of the C.lucidus. |
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