Probe Design For Target Enrichment In Acrididae And Hymenoptera

Target enrichment sequencing is a way of using the customize probes to capture target sequences.Customize probes are designing for a specific subset of the selected genome.Because of relatively low quality requirements for specimens and can exclude other bases such as paralogs gene,repeat sequences interference,Target enrichment sequencing is widely used in the phylogeny studies.The crucial thing is to design and select target probes in target enrichment sequencing.However,in many clades(e.g.Orthoptera),there are no available targeted probes due to the lack of genomic resources.On the other hand,there are various kinds of targeted probes available in genomic resource-rich clades(e.g.Hymenoptera),causing researchers difficult for choosing probes.Therefore,how to design and select a reliable targeted probe has been widely concerned and discussed by researchers.Based on the six locust genomes,the UCE probes of grasshoppers were developed and designed.Then,we also designed a set of RELEC probes for Hymenoptera via 11 genomes from NCBI databases.Among the study,we fouse on the effects of data filtering and capture makers select on phylogenetic reconstruction.The main results are as following:(1)The UCE probes of grasshoppersOnly one genome of Acridoidea was published in the beginning of the study of in order to design the UCE probes of grasshoppers,we need more extra genomes.Five locust genomes were low coveraged sequenced and assembled including Oxya chinensis,Calliptamus abbreviates,Chondracris rosea,Haplotropis brunneriana and Atractomorpha sinensis.The assembled genome sizes were from 8.00 Gb to 15.32 Gb.Their contigs N50 were 904 bp-1583 bp and BUSCOs completes were 13.6%-29.7%.Combining the genomes of Locusta migratoria,a total of 4,065 UCE locus were identified,and 12615 probes were designed after removing the duplicate sequences.The phylogenetic tree of the six locusts constructed via the UCE probes capturing is consistent with the results of previous morphology and molecular studies.We further filtered the UCE baits of the design based on six attributes,including sequence length,RCVF,GC content,C value,PIS value,and missing data,analyzed phylogenetic tree reconstruction by the data filtering.We found that the UCE locus had higher node support and gene tree consistency after data filtering.The correlation between these six attributes is weak,which means that each property should be considered when filtering UCE locus.(2)The RELEC probes of HymenopteraIn this study,11 representative species genomes of Hymenoptera were analyzed and compared,177 rapidly evolving long exon(RELEC)locus were gained finally.This study compared the newly designed RELEC probe with the other two commonly used targeted probes(AHE and UCE)for Hymenoptera and found that most of the system development tree nodes recovered by these three probes was similarly to previous studies.Only in the ant colony,all three probes do not have very good node support,which may be due to the existence of incomplete lineage sorting.This study further analyzed the relationship between node supports,gene tree and species tree consistency of the three data sets and found that RELEC performed best in all probes.Statistical analysis of the locus of each data set shows that the newly designed RELEC bits perform well in all aspects.The number of locus is small and is less affected by genetic recombination factors.Considering that RELEC is a good target enrichment approach for groups of sufficient genomic resources,such as Hymenoptera.In this paper,the target enrichment probe is designed for two types of insects,locusts and Hymenoptera.These two groups represent the current genomic resources and abundant groups.This paper not only compares the effects and patterns of the phylogenetic reconstruction before and after data filtering,but also compares the performance of different data sets in the same species.These conclusions provide novel inspiration to design new target enrichment probes and to understand the evolution between locusts and Hymenoptera.