Expression Analysis of Apocheima cinerarius Ershoff from Different Geographical Populations through Illumina RNA-seq
Expression Analysis of Apocheima cinerarius Ershoff from Different Geographical Populations through Illumina RNA-seq
Lei Wang1, Lu Yang2, Lei Luo1, Yaqi Gao1*, Jian Gao1 and Ping Liu1
ABSTRACT
This study elucidated the differences between Apocheima cinerarius Ershoff (1874)populations from various geographic regions (southern and northern Xinjiang) based on morphological features, biological characteristics, and gene expression, thus providing a theoretical basis for the genetic manipulation of A. cinerarius. Illumina RNA-Seq was used to perform massive sequencing of 18 cDNA samples derived from male adults, female adults, and pupa of A. cinerarius in southern and northern Xinjiang. We extracted total RNA from 18 samples and synthesized cDNA via reverse transcription. Then, Illumina sequencing was performed and unigenes were identified after assembly and clustering. The resulting unigenes were then compared to homologous sequences using NCBI-NR, Swiss-Prot, KOG, Pfam, eggNOG, KEGG, COG, and GO for functional annotation and classification. Some differences in the regularity of distribution and the time of eclosion of the pupa were detected between the southern and the northern populations. We obtained 142.65 Gb of data from transcriptome sequencing and recovered 70,397 unigenes through a de novo assembly. In total, 2089, 2420, and 6286 differentially expressed genes were gained from comparing groups of male adults, female adults, and pupa of A. cinerarius, respectively. In addition, 27715 SSR markers were obtained and the SNP site was identified. The results revealed the differences between A. cinerarius in southern and northern Xinjiang, enriches the genetic information of A. cinerarius, and accelerates research aimed at addressing the regularity of genetic variations.
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October 2020
Vol. 52, Iss. 5, Pages 1631-2026
