| Hyriopsis schlegelii,Hyriopsis cumingii,Cristaria plicata and Anodonta woodiana are mainly pearl mussels in China.Among them,H.schlegelii and H.cumingii have the best effect of cultivating pearls.There are two key problems that have not been solved in the comparative study of H.schlegelii and H.cumingii:Firstly,The genetic relationship between H.cumingii and H.cumingii has always been controversial.Secondly,studies have shown that H.schlegelii is superior to H.cumingii in terms of survival rate,disease resistance and performance of pearl breading,but the molecular mechanism is still unclear.This study aims to study the molecular mechanism of H.schlegelii in terms of growth and development,pearl breading and disease resistance and its relationship with other freshwater pearls from the perspective of transcriptomics.In this study,the transcriptomes of four species of freshwater mussels were sequenced(NGS)by illumine and then conducted de novo assembly.The Unigenes of four species of freshwater mussels were translated into protein sequences and then blast to EggNOG database for functional annotation.The results of the annotation indicate that the distribution of these four species in COG classification was similar,Among them,the most abundant genes are classified into "S:function unknown" and "signal transduction mechanism"(T:signal transduction mechanisms).A total of 29,468 potential homologous gene families were identified in four freshwater pearls,and and the 16001 homologous gene families shared by four species constitute the core genes set of freshwater pearls.These core genes participate in a wide range of basic activities,almost distributed in every GO function.There are 5175 homologous gene families that exist only between H.schlegelii and H.cumingii.In addition,the number of unique gene families is 12,11,9,and 15,respectively.In order to further analyze the phylogeny of freshwater pearl mussels,in this study,we conducted comparative transcriptomic analysis between H.schlegelii and its relatives,including H.cumingii,A.woodiana and C.plicata.The genetic distance between the four freshwater pearl mussels was calculated after the multiple sequence alignment(MSA)of their shared single-copy orthologs.The results showed that the genetic distance between H.schlegelii and H.cumingii was only 0.00746(<1%),while the genetic distance between other freshwater pearl mussels was almost 10 times higher than that.Phylogenetic analysis showed that Ambleminae and Anodontinae diverged approximately 51.44 million years ago(Mya),while H.schlegelii and H.cumingii were divided about 4.24 million years ago.Further analysis identified the specific genes in the transcriptome of H.schlegelii.The enrichment of the KEGG pathway indicated that these genes were mainly enriched in the pathways such as CD molecules and protein digestion and absorption.Moreover,GO annotation results showed that there were many specific genes related to excellent characters of H.schlegelii,including development-related biological process such as developmental process,system development,animal organ development,and immune-related biological process such as immune system process and antigen processing and presentation in GO classification.In this study,several pathways related to the growth and development,immunity and disease resistance were found by analyzing the specific genes of H.schlegelii at the same time.The KEGG pathway enrichment analysis of the specific genes of H.schlegelii showed that the genes were mainly enriched in the pathways of CD molecules,protein digestion and absorption.Several specific genes in the H.schlegelii were detected by real-time qPCR,and the results were consistent with the results of the transcriptomic analysis.Additionally,the pathway of protein digestion andabsorption and NF-κB signaling pathway in the mussel were predicted.The above results showed that H.schlegelii and H.cumingii have closer genetic relationship,and they may be different subspecies or populations,which has important reference significant for the germplasm conservation and genetic breeding of freshwater pearl mussels.Additionally,compared to H.cumingii,H.schlegelii may have several specific genes related to development and immunity,which provided some clues for exploring the related molecular mechanism. |
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