Abstract
Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. They represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (FL) PacBio transcriptome sequencing. For G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (FLNC) reads. After isoform-level clustering, next-generation sequencing (NGS) short sequences were used for error correction, and remove redundant sequences with CD-HIT, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. In addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research.
Highlights
One important goal of functional genomics is to establish relationships between genotypes and phenotypes based on genomic sequence information and various omics techniques[1]
After isoform-level clustering based on the iterative clustering for error correction (ICE) algorithm and polishing based on the Arrow algorithm, a total of 29,340 polished FL consensus isoforms with an average length of 2,995 bp were generated from the full-length nonchimeric (FLNC) reads, including 28,736 high-quality (HQ; accuracy ratio > 99%) and 601 low-quality (LQ; accuracy ratio ≤ 99%) sequences (Table 1)
After redundancy removal via the CD-HIT program and filtering reads less than 200 bp in length, the consensus isoforms were clustered into a total of 17,932 unigenes for subsequent analysis (Table 1)
Summary
One important goal of functional genomics is to establish relationships between genotypes and phenotypes based on genomic sequence information and various omics techniques[1]. The rapid development of high-throughput sequencing technology has greatly facilitated the study of functional genomics, especially the completion of genome sequencing of a large number of species 2–5. RNA-seq has been applied to a large number of species and studies, short-read (e.g., reads obtained from Illumina sequencing platforms) sequencing does not provide full-length (FL) transcript sequences due to its inherent length limitations, thereby limiting its utility. Due to the much longer read lengths of PacBio sequencing, the precise locations and sequences of repetitive regions and isoforms can often be resolved with a single read. The Acrididae fauna of most regions is well known, and a worldwide taxonomic file is available (https://Orthoptera.SpeciesFile.org)[15]; these features make Acrididae a good subject for the study of phylogeny and evolution. For the migratory locust Locusta migratoria (genome size is ~ 6.5 Gb) is a complete genome sequence available far[17]
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