Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis

Jojoba is one of the main two known plant source of natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to the lack of transcriptomic and genomic data on lipid biosynthesis and accumulation, molecular marker breeding has been used to improve jojoba oil production and quality. In the current study, the transcriptome of developing jojoba seeds was investigated using the Illunina NovaSeq 6000 system, 100 × 106 paired end reads, an average length of 100 bp, and a sequence depth of 12 Gb per sample. A total of 176,106 unigenes were detected with an average contig length of 201 bp. Gene Ontology (GO) showed that the detected unigenes were distributed in the three GO groups biological processes (BP, 5.53%), cellular component (CC, 6.06%), and molecular functions (MF, 5.88%) and distributed in 67 functional groups. The lipid biosynthesis pathway was established based on the expression of lipid biosynthesis genes, fatty acid (FA) biosynthesis, FA desaturation, FA elongation, fatty alcohol biosynthesis, triacylglycerol (TAG) biosynthesis, phospholipid metabolism, wax ester biosynthesis, and lipid transfer and storage genes. The detection of these categories of genes confirms the presence of an efficient lipid biosynthesis and accumulation system in developing jojoba seeds. The results of this study will significantly enhance the current understanding of wax ester biology in jojoba seeds and open new routes for the improvement of jojoba oil production and quality through biotechnology applications.

De novo assembly and annotation of the eastern fence lizard (Sceloporus undulatus) transcriptome

BackgroundThe eastern fence lizard (Sceloporus undulatus) has been a model species for ecological and evolutionary research. Genomic and transcriptomic resources for this species would promote investigation of genetic mechanisms that underpin plastic responses to environmental stress, such as climate warming. Moreover, such resources would aid comparative studies of complex traits at the molecular level, such as the transition from oviparous to viviparous reproduction, which happened at least four times within Sceloporus.FindingsA de novo transcriptome assembly for Sceloporus undulatus, Sund_v1.0, was generated using over 179 million Illumina reads obtained from three tissues (whole brain, skeletal muscle, and embryo) as well as previously reported liver sequences. The Sund_v1.0 assembly had an average contig length of 782 nucleotides and an E90N50 statistic of 2,550 nucleotides. Comparing S. undulatus transcripts with the benchmarking universal single-copy orthologs (BUSCO) for tetrapod species yielded 97.2% gene representation. A total of 13,422 protein-coding orthologs were identified in comparison to the genome of the green anole lizard, Anolis carolinensis, which is the closest related species with genomic data available.ConclusionsThe multi-tissue transcriptome of S. undulatus is the first for a member of the family Phrynosomatidae, offering an important resource to advance studies of adaptation in this species and genomic research in reptiles.

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomics projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample, which averaged 1319 nt in length and 99.7 % accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62 % of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.