High-quality chromosome-level genome assembly of redlip mullet (<i>Planiliza haematocheila</i>)

Abstract

A: K-mer survey of P. haematocheila genome. B: Heat map of Hi-C assembly of P. haematocheila . Red blocks refer to intensity of interactions among sequences, blue blocks refer to boundaries of chromosomes, and green blocks refer to assembly scaffolds. C: Genome synteny analysis between novel chromosome sequences and top 30 longest contigs of previously published P. haematocheila genome. D: Distribution of GC content and sequencing depth of P. haematocheila genome. E: Statistics of exon number and length of different gene structures in P. haematocheila and several reference species. Different colors represent different species. F: Gene family cluster results of P. haematocheila and nine other reference species. Abscissa represents species and ordinate represents number of genes. G: Phylogenetic tree estimates of divergence time and interval based on sequence identity are indicated at each node. Estimated number of orthologous gene groups in most recent common ancestral (MRCA) species is shown at root. Numbers of gene families expanded or contracted in each lineage are shown on corresponding branch; +, expansion; −, contraction. H: GO enrichment analysis of significantly expanded gene families. I: KEGG pathway enrichment analysis of significantly expanded gene families.

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

“…The functional annotation of predicted protein-coding genes was performed using BLAST (blastp) with an e-value of 1 × 10 −5 against several databases [44]: the SWISS-PROT database [45], the NCBI non-redundant protein (NR) database, the Translated EMBL (TrEMBL) database, the Clusters of Orthologous Genes (COG) database, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database [46]. Additionally, protein motifs and domains were annotated by searching the InterPro and Gene Ontology (GO) databases using InterProScan (v.4.8) [47].…”

First Report of Chromosome-Level Genome Assembly for Flathead Grey Mullet, Mugil cephalus (Linnaeus, 1758)

“…Comparative genome analysis was performed to characterize genome-wide syntenic regions between redlip mullet (Zhao et al, 2021) and grey mullet (this study) genomes. The 24 chromosome-level scaffolds of the redlip mullet assembly (648.41 Mb) obtained from the China National Gene Bank Database (CNGBdb: CNP0001604) were aligned to the 24 pseudo-chromosomes of the grey mullet assembly (634.84 Mb) using SyMAP 4.2 (Soderlund et al, 2006).…”

“…Within the family Mugilidae, a draft genome assembly was first reported for redlip mullet, Liza haematocheila (0.74 Gb), which has 1,453 contigs with an N50 length of 3.9 Mb (Liyanage et al, 2019). Later, chromosome-level assembly of this fish was generated with Oxford Nanopore long-read, single-tube long fragment reads (stLFR), and HiC chromatin interaction data, which are 652.91 Mb length in 514 scaffolds with contig and scaffold N50 lengths of 7.21 and 28.01 Mb, respectively (Zhao et al, 2021). For M. cephalus, no whole-genome assembly with long-read data is available.…”