The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource

Abstract

The tea aphid, Aphis aurantii , has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of A. aurantii was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of A. aurantii . It will assist the future functional study of genes involved in its development and reproduction.

Full-length transcriptome analysis of Adiantum flabellulatum gametophyte

“…The FLNC sequences from the same copy were grouped into clusters, and the Arrow algorithm ( Hong et al, 2020 ) was used to correct the error. After removing the low-quality sequences, 2,608,705 consensus reads were obtained with an average quality of 0.99 ( Fig.…”

Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

“…For a non-model diatom without a reference genome, SGS sequencing is inadequate for producing an FL transcriptome. PacBio sequencing has been used to analyse the FL transcriptome of animals and higher plants [ 29 , 30 ]. The T. weissflogii FL transcriptome here represents the first general transcription encyclopaedia of the species and FL transcriptome from a diatom.…”

“…However, the detection of AS events in this study was limited due to the lack of a reference genome of T. weissflogii . This would result in the missing and underestimation of some types of AS [ 29 ]. An SSR or microsatellite is a repetitive DNA sequence where certain motifs are repeated.…”

Single-Molecule Long-Read Sequencing Facilitates Transcriptomic Research For Whitmania Pigra, The Most Utilized Medical Leech In Chinese Traditional Medicine For Anticoagulant Therapy

“…This will inevitably introduce misinterpretations to different isoforms and may merge different members of multigene families. Also, the short-read transcriptomes could not resolve important factors such as isoforms, long-non-coding RNAs (lncRNA), and alternative splicing (AS) events, which limits the understanding of the deeper meaning of related life activities (Rhoads and Au, 2015;Weirather et al, 2017;Hong et al, 2020). The anticoagulant repertoire obtained from these studies is relatively unitary, leaving room for further improvement of accuracy.…”

“…Previous studies have noted the importance of accurate molecular sequences in exploring the genetic foundation of biological characters. The advantages of long-read sequencing technology represented by PacBio have been extensively demonstrated by recent studies(Grabherr et al, 2011;Rhoads and Au, 2015;Byrne et al, 2019;Zhang et al, 2019;Hong et al, 2020). The long-read sequencing technology can enrich and/or improve the current molecular sequences for a given organism.…”