Comprehensive transcriptome analysis of sika deer antler using PacBio and Illumina sequencing

Abstract

Antler is the fastest growing and ossifying tissue in animals and it is a valuable model for cartilage/bone development. To understand the molecular mechanisms of chondrogenesis and osteogenesis of antlers, the PacBio Sequel II and Illumina sequencing technology were combined and used to investigate the mRNA expression profiles in antler tip, middle, and base at six different developmental stages, i.e., at 15th, 25th, 45th, 65th, 100th and 130th growth days. Consequently, we identified 24,856 genes (FPKM > 0.1), including 8778 novel genes. Besides, principal component analysis (PCA) revealed a significant separation between the growth stage (25th, 45th and 65th days) and ossification stage (100th and 130th days). COL2A1 gene was significantly abundant in the growth stage, whereas S100A7, S100A12, S100A8, and WFDC18 genes were abundant at the ossification stage. Subsequently screened to 14,765 significantly differentially expressed genes (DEGs), WGCNA and GO functional enrichment analyses revealed that genes related to cell division and chondrocyte differentiation were up-regulated, whereas those with steroid hormone-mediated signaling pathways were down-regulated at ossification stages. Additionally, 25 tumor suppressor genes and 11 oncogenes were identified and were predicted to interact with p53. Co-regulation of tumor suppressor genes and oncogenes is responsible for the special growth pattern of antlers. Together, we constructed the most complete sika deer antler transcriptome database so far. The database provides data support for subsequent studies on the molecular mechanism of sika deer antler chondrogenesis and osteogenesis.

Combined transcriptome and proteome analyses between the cytoplasmic male sterile line and its maintainer line in Welsh onion (Allium fistulosum)

“…Meanwhile, transcripts annotated databases to obtain the function of transcripts. These results indicate that PacBio transcriptome sequencing can augment the ability to acquire comprehensive flower‐specific transcripts, improve upland Welsh onion genome annotation, and enrich new or unidentified isoforms or genes, which were consistent with previous researches (Rhoads & Au, 2015; Zhang et al, 2022).…”

A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development

“…Transcription factors (TFs) are responsible for phenotypic changes by controlling the expression of trait-associated genes [ 15 , 16 ]. To study the regulation of TFs on the development of antler, we reanalysed the RNA-seq data published by zhang et al [ 17 ]. The hmmsearch program was used to identify TFs in all protein sequences of sika deer based on AnimalTFDB (v2.0) database.…”

“…PAX2, SIX4, SIX6, SOX8, SPI1, JDP2, ZNF170, NFAC1 are all important regulatory factors involved in the process of cell proliferation and development [ 24 – 28 ], playing crucial roles in the development of deer antlers as well. Compared to the transcriptome analysis conducted by Zhang et al [ 17 ], our re-analysis the RNA data has yielded novel insights. Firstly, our re-analysis has once again confirmed the reliability of the consensus genome, identifying a total of 24,127 expressed genes (FPKM > 0.1), including 3,126 novel genes (12.96%).…”

“…Subsequently, these TFs were classified into 57 families based on the animalTFDB database. zf-C2H2 (158), Homeobox (64), ZBTB (53), bHLH (51), TF_bZIP (29), HMG (28), Forkhead box (24), ETS (17), MYB (15), and THR-like (11) were possessed more than 10 copies. Notably, the zf-C2H2 exhibited a remarkable 158 copies.…”