Phylogeny Of Goniopora Lobata Based On Mitochondrial Genome And Ultra-conserved Elements

Stony corals are the main constructive species of coral reef communities,so studying the phylogeny of stony coral has a great significance to the protect of coral reef resources.In this study,Next Generation Sequencing(NGS)was used to obtain mitochondrial genomic data of Goniopora lobata,and based on this,the evolutionary relationship of the order Scleractinia was constructed.At the same time,based on the genomic data of the order Scleractinia and Corallimorpharia,the ultra-conserved elements of the stony corals were identified whose probes of the ultra-conserved elements of the stony corals also were designed,and the data of the ultra-conserved elements were used to study phylogeny.The main research results are as follows:1.The total length of the assembled Goniopora lobata genomic dataset(coverage is about 10%)is 62,270,395 bp,which includes the Goniopora lobata mitochondrial genome with sizes of 18,770 bp,GC content is 37.01%,The proportions of base A,C,G and T in total bases were 25.72%,13.59%,23.42%,and 37.27%.Mitochondrial genes consist of 13 protein-coding genes,3 t RNA genes and 2 ribosomal RNA genes.Based on mitochondrial genomes of the order Scleractinia,a phylogenetic tree was constructed.The evolution distance between Goniopora lobata and the other Genus Goniopora animals;Goniopora djiboutiensis and Goniopora columna,is about 0.0101.The genus Goniopora is branched from the family Poritidae about 117 million years ago,,and the Goniopora lobata have diverged from the ancestors of the genus Goniopora for more than 20 million years.2.We used Acropora millepora genome as the reference genome,based on the PHYLUCE process,combined with other stony coral animal genomes to identify and obtain 3,561 ultra-conservative elements Scleractinia UCE in the order Scleractinia,and there are 1,439 ultra-conserved elements coral UCE in the order Scleractinia and Corallimorpharia.More than 98% of the ultra-conserved elements mainly fall in the gene region rather than the intergenic region at the order Scleractinia genome.GO enrichment analysis results show that these conserved elements mainly involve the cytoskeleton,protein metabolism,m RNA processing,chromosome modification,and early embryo development,which are mainly upstream regulatory genes.3.A total of 42,377 probes,Scleractinia-v2-master-probe,were designed according to the ultra-conserved elements of the order Scleractinia and a total of 22,910 probes,coral-v2-master-probes,were designed according to ultra-conserved elements shared by the order Scleractinia and Corallimorpharia.Those data verified that both probes can be used for the study of ultra-conserved elements in the order Scleractinia.4.According to the ultra-conserved elements of the order Scleractinia,build a phylogenetic tree and split network diagram to study the phylogeny of Goniopora lobata.It was found that the reticulate structure diagram based on stony coral ultraconserved elements suggested that there might be branches in the clade of robust stony corals;the location of Goniopora lobata in the reticulate structure diagram based on the ultra-conserved elements shared by the order Scleractinia and Corallimorpharia is between Nematostella vectensis and the complex clade of stony coral.In this study,through the application of low-coverage genome data and the identification and probe design of coral ultra-conserved elements,it is hoped that it can supplement the research ideas for the phylogeny of stony coral and provide some data support for the study of ultra-conserved elements in the order Scleractinia.