Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle

Understanding of molecular basis of histological graded horn cancer by transcriptome profiling

Horn cancer is most devastating and prominent cancer in Indian zebu cattle that affects socio-economic condition of small-scale farmers who depends on their cattle for farm work. Development in the field for genomics through next generation sequencing and bioinformatics advancement have helped to identify genes which have a role in horn cancer development. Histopathological examination of cancerous tissues of horn revealed myxomatous changes, well, moderate and poorly differentiated squamous cell carcinoma. Differential gene expression analysis showed 40, 11, 66 and 29 upregulated genes and 10, 14, 08 and 07 down-regulated genes in myxomatous, well, moderate and poorly differentiated squamous cell carcinoma as compared to normal. Significant differentially expressed genes are related to cell development, cell proliferation, cell-cell communication, cell signaling and angiogenesis which are linked to Akt pathway, mTOR pathway and Wnt pathway. Activity of these genes and related pathways have already been established about their role in development of cancer. Among the candidate genes; keratin family, keratin family related gene, chemokine signaling and cytokines signaling associated genes could be a prominent target for the development of stage specific prognosis marker after further detailed study at large sample population level. CSTA, PTN, SPP1 genes have upregulation in all stages of cancer and they have enrolled as biomarkers for horn cancer.

De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

The sequenced data availability opened new horizons related to buffalo genetic control of economic traits and genomic diversity. The visceral organs (brain, liver, etc.) significantly involved in energy metabolism, docility, or social interactions. We performed swamp buffalo transcriptomic profiling of 24 different tissues (brain and non-brain) to identify novel transcripts and analyzed the differentially expressed genes (DEGs) of brain vs. non-brain tissues with their functional annotation. We obtained 178.57 Gb clean transcriptomic data with GC contents 52.77%, reference genome alignment 95.36%, exonic coverage 88.49%. Totally, 26363 mRNAs transcripts including 5574 novel genes were obtained. Further, 7194 transcripts were detected as DEGs by comparing brain vs. non-brain tissues group, of which 3,999 were upregulated and 3,195 downregulated. These DEGs were functionally associated with cellular metabolic activities, signal transduction, cytoprotection, and structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, JAK-STAT signaling, basic cellular metabolism, thermogenesis, and oxidative phosphorylation. Our study provides an in-depth understanding of swamp buffalo transcriptomic data including DEGs potentially involved in basic cellular activities and development that helped to maintain their working capacity and social interaction with humans, and also, helpful to disclose the genetic architecture of different phenotypic traits and their gene expression regulation.

Molecular portrait of squamous cell carcinoma of the bovine horn evaluated by high-throughput targeted exome sequencing: a preliminary report

Background

Squamous Cell Carcinoma of horn, also known as horn cancer, is a prevailing type of cancer in cattles especially Bos indicus. It is one of the most prevalent disease in Indian bullocks often resulting in death and huge economic losses to farmers. Here, we have reported the use of targeted exome sequencing to identify variants present in horn cancer affected horn mucosa tissue and blood of the same animal to identify some of the prevalent markers of horn cancer.

Results

We have observed higher number of variants present in tissue as compared to blood as well as among cancer samples compared to samples from normal animals. Eighty six and 1437 cancer-specific variants were identified among the predicted variants in blood and tissue samples, respectively. Total 25 missense variants were observed distributed over 18 genes. KRT8 gene coding for Keratin8, one of the key constituents of horn, displayed 5 missense variants. Additionally, three other genes involved in apoptosis pathway and two genes involved in antigen presentation and processing also contained variants.

Conclusions

Several genes involved in various apoptotic pathways were found to contain non-synonymous mutations. Keratin8 coding for Keratin, a chief constituent of horn was observed to have the highest number of mutations. In all, we present a preliminary report of mutations observed in horn cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-020-02683-y.

Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis

The goal of this study was to identify differentially expressed genes (DEGs) responsible for peanut plant (Arachis hypogaea) defence against Puccinia arachidis (causative agent of rust disease). Genes were identified using a high-throughput RNA-sequencing strategy. In total, 86,380,930 reads were generated from RNA-Seq data of two peanut genotypes, JL-24 (susceptible), and GPBD-4 (resistant). Gene Ontology (GO) and KEGG analysis of DEGs revealed essential genes and their pathways responsible for defence response to P. arachidis. DEGs uniquely upregulated in resistant genotype included pathogenesis-related (PR) proteins, MLO such as protein, ethylene-responsive factor, thaumatin, and F-box, whereas, other genes down-regulated in susceptible genotype were Caffeate O-methyltransferase, beta-glucosidase, and transcription factors (WRKY, bZIP, MYB). Moreover, various genes, such as Chitinase, Cytochrome P450, Glutathione S-transferase, and R genes such as NBS-LRR were highly up-regulated in the resistant genotype, indicating their involvement in the plant defence mechanism. RNA-Seq analysis data were validated by RT-qPCR using 15 primer sets derived from DEGs producing high correlation value (R ² = 0.82). A total of 4511 EST-SSRs were identified from the unigenes, which can be useful in evaluating genetic diversity among genotypes, QTL mapping, and plant variety improvement through marker-assisted breeding. These findings will help to understand the molecular defence mechanisms of the peanut plant in response to P. arachidis infection.

Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus)

Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.

Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.)

Cytoplasmic Male Sterility is maternally inherited trait in plants, characterized by failure to produce functional pollen during anther development. Anther development is modulated through the interaction of nuclear and mitochondrial genes. In the present study, differential gene expression of floral buds at the sporogenous stage (SS) and microsporocyte stage (MS) between CGMS and its fertile maintainer line of cotton plants was studied. A total of 320 significantly differentially expressed genes, including 20 down-regulated and 37 up-regulated in CGMS comparing with its maintainer line at the SS stage, as well as and 89 down-regulated and 4 up-regulated in CGMS compared to the fertile line at MS stage. Comparing the two stages in the same line, there were 6 down-regulated differentially expressed genes only induced in CGMS and 9 up-regulated differentially expressed gene only induced in its maintainer. GO analysis revealed essential genes responsible for pollen development, and cytoskeleton category show differential expression between the fertile and CGMS lines. Validation studies by qRT-PCR shows concordance with RNA-seq result. A set of novel SSRs identified in this study can be used in evaluating genetic relationships among cultivars, QTL mapping, and marker-assisted breeding. We reported aberrant expression of genes related to pollen exine formation, and synthesis of pectin lyase, myosine heavy chain, tubulin, actin-beta, heat shock protein and myeloblastosis (MYB) protein as targets for CMS in cotton. The results of this study contribute to basic information for future screening of genes and identification of molecular portraits responsible for CMS as well as to elucidate molecular mechanisms that lead to CMS in cotton.

De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery

Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an average length of 641 bp were obtained and 19,915 unigenes were successfully annotated in four public databases. Only 9932 out of 19915 unigenes were commonly annotated by all four databases. In addition, 9609 unigenes were categorized into 54 function categories of Gene Ontology (GO), and 14,512 unigenes were successfully grouped into 25 functional categories of the EuKaryotic Orthologous Groups (KOG) database. Moreover, 11,507 unigenes were assigned to 228 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Out of 51,092 unigenes, a total of 4257 different microsatellites with motifs range from di- to hexa-nucleotide were identified from 3324 unigene sequences. Among 64 primer pairs selected for validation, 35 were successful in PCR amplification and 13 exhibited obvious repeat polymorphisms in the wild population of S. terebrans in Dongzhaigang (Hainan Island). The transcriptome dataset and the identified microsatellite markers (SSRs) will provide abundant information for researches on the discovery of new genes, metabolic mechanism and genetic diversity of S. terebrans.

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

BACKGROUND

RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver tissue of young bulls of the Polish Red, Polish Holstein-Friesian (HF) and Hereford breeds, and to understand the genomic variation in the three cattle breeds that may reflect differences in production traits.

RESULTS

The RNA-seq experiment on bovine liver produced 107,114,4072 raw paired-end reads, with an average of approximately 60 million paired-end reads per library. Breed-wise, a total of 345.06, 290.04 and 436.03 million paired-end reads were obtained from the Polish Red, Polish HF, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed that 81.35%, 82.81% and 84.21% of the mapped sequencing reads were properly paired to the Polish Red, Polish HF, and Hereford breeds, respectively. This study identified 5,641,401 SNPs and insertion and deletion (indel) positions expressed in the bovine liver with an average of 313,411 SNPs and indel per young bull. Following the removal of the indel mutations, a total of 195,3804, 152,7120 and 205,3184 raw SNPs expressed in bovine liver were identified for the Polish Red, Polish HF, and Hereford breeds, respectively. Breed-wise, three highly reliable breed-specific SNP-databases (SNP-dbs) with 31,562, 24,945 and 28,194 SNP records were constructed for the Polish Red, Polish HF, and Hereford breeds, respectively. Using a combination of stringent parameters of a minimum depth of ≥10 mapping reads that support the polymorphic nucleotide base and 100% SNP ratio, 4,368, 3,780 and 3,800 SNP records were detected in the Polish Red, Polish HF, and Hereford breeds, respectively. The SNP detections using RNA-seq data were successfully validated by kompetitive allele-specific PCR (KASPTM) SNP genotyping assay. The comprehensive QTL/CG analysis of 110 QTL/CG with RNA-seq data identified 20 monomorphic SNP hit loci (CARTPT, GAD1, GDF5, GHRH, GHRL, GRB10, IGFBPL1, IGFL1, LEP, LHX4, MC4R, MSTN, NKAIN1, PLAG1, POU1F1, SDR16C5, SH2B2, TOX, UCP3 and WNT10B) in all three cattle breeds. However, six SNP loci (CCSER1, GHR, KCNIP4, MTSS1, EGFR and NSMCE2) were identified as highly polymorphic among the cattle breeds.

CONCLUSIONS

This study identified breed-specific SNPs with greater SNP ratio and excellent mapping coverage, as well as monomorphic and highly polymorphic putative SNP loci within QTL/CGs of bovine liver tissue. A breed-specific SNP-db constructed for bovine liver yielded nearly six million SNPs. In addition, a KASPTM SNP genotyping assay, as a reliable cost-effective method, successfully validated the breed-specific putative SNPs originating from the RNA-seq experiments.

Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology

Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform the detection of SNPs in the pituitary gland of young growing bulls representing Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds at three developmental ages viz., six months, nine months, and twelve months. A total of 18 bovine pituitary gland polyA transcriptome libraries were prepared and sequenced using the Illumina NextSeq 500 platform. Sequenced FastQ databases of all 18 young bulls were submitted to NCBI-SRA database with NCBI-SRA accession numbers SRS1296732. For the investigated young bulls, a total of 113,882,3098 raw paired-end reads with a length of 156 bases were obtained, resulting in an approximately 63 million paired-end reads per library. Breed-wise, a total of 515.38, 215.39, and 408.04 million paired-end reads were obtained for Polish HF, Polish Red, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed 93.04%, 94.39%, and 83.46% of the mapped sequencing reads were properly paired to the Polish HF, Polish Red, and Hereford breeds, respectively. Constructed breed-specific SNP-db of three cattle breeds yielded at 13,775,885 SNPs. On an average 765,326 breed-specific SNPs per young bull were identified. Using two stringent filtering parameters, i.e., a minimum 10 SNP reads per base with an accuracy ≥ 90% and a minimum 10 SNP reads per base with an accuracy = 100%, SNP-db records were trimmed to construct a highly reliable SNP-db. This resulted in a reduction of 95,7% and 96,4% cut-off mark of constructed raw SNP-db. Finally, SNP discoveries using RNA-Seq data were validated by KASP^™ SNP genotyping assay. The comprehensive QTLs/CGs analysis of 76 QTLs/CGs with RNA-seq data identified KCNIP4, CCSER1, DPP6, MAP3K5 and GHR CGs with highest SNPs hit loci in all three breeds and developmental ages. However, CAST CG with more than 100 SNPs hits were observed only in Polish HF and Hereford breeds.These findings are important for identification and construction of novel tissue specific SNP-db and breed specific SNP-db dataset by screening of putative SNPs according to QTL db and candidate genes for bovine growth and reproduction traits, one can develop genomic selection strategies for growth and reproductive traits.

Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing

The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget.

De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery

The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.