Genomics and Transcriptomics

Genomics explores the full complement of genetic material within an organism, examining genome structure, sequence variation and functional elements. Advances in high-throughput and single-molecule sequencing have enabled rapid assembly of reference genomes and sensitive detection of mutations ranging from single-nucleotide polymorphisms to large structural variants. Complementarily, transcriptomics employs methods such as RNA-Seq and microarrays to profile the transcriptome—the complete set of RNA transcripts—across tissues, stages or conditions. Together, these approaches illuminate how genetic variation influences gene expression, regulatory networks, alternative splicing and non-coding RNA function. Integration of genomic and transcriptomic data accelerates gene annotation, reveals expression quantitative trait loci, and underpins applications in precision breeding, personalised medicine and fundamental studies of evolution and development.

Research from Nature Portfolio

Fine-scale mapping of recombination in threespine stickleback fish uncovered pronounced heterochiasmy between sexes and ecotype-specific crossover suppression at adaptive loci, linking recombination landscapes to natural selection and fitness differences. In rice, a graded-pool sequencing strategy enabled rapid localisation and cloning of a major heterotic quantitative trait locus that, when introgressed into an elite inbred line, delivered substantial yield gains, illustrating a streamlined pipeline for translating recombination mapping into crop improvement. Large-scale human studies have produced sex-specific genetic maps from over 100,000 meioses, revealing that although most hotspots are shared, subtle differences in hotspot intensity and telomeric bias contribute to variation in inheritance patterns and inform models of recombination-associated disease risk.

Research from all publishers

A barley mutant with a chlorophyll-deficient phenotype was dissected using a whole-genome shotgun approach coupled to bulked segregant analysis, pinpointing a novel allele of the chlorophyll synthase gene and demonstrating the efficacy of rapid causal-mutation pipelines in cereals. In lentil, whole-genome resequencing of early- and late-flowering bulks identified three loci governing maturity and led to the development of an insertion/deletion marker in the ELF3a gene, offering a tool for breeding early-maturing lines suited to terminal-drought conditions. In population genetics, evaluations of sequentially Markov coalescent methods showed that accurate genome-average recombination rates can be inferred from single diploid genomes—provided one accounts for within-genome heterogeneity and gene conversion—thereby enhancing the utility of modestly sized sequencing projects for estimating effective population parameters.

Genomics and Transcriptomics publication trend

The graph below shows the total number of articles in genomics and transcriptomics across all publications each year (not limited to Nature Index journals).

Technical terms

Next-generation sequencing (NGS): High-throughput platforms that generate large volumes of DNA sequence data in parallel, enabling rapid genome assembly and variant discovery.

Quantitative trait locus (QTL): A genomic region statistically associated with variation in a quantitative phenotype, such as yield, flowering time or stress tolerance.

Bulked segregant analysis (BSA): A mapping method in which DNA (or RNA) from groups of individuals with contrasting phenotypes is pooled and sequenced to identify linked genetic markers.

Contig: A contiguous consensus sequence assembled from overlapping sequencing reads without gaps.

Scaffold: A series of ordered and oriented contigs linked by paired-end or mate-pair information, approximating chromosomal segments.

Recombination hotspot: A discrete genomic interval exhibiting a significantly elevated frequency of meiotic crossover events.

RNA-Seq: The sequencing of cDNA derived from RNA samples to quantify transcript abundance and discover novel transcripts or splicing variants.

References

1. Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. Nature Ecology & Evolution (2024).
2. Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy. Nature Communications (2019).
3. Refined genetic maps reveal sexual dimorphism in human meiotic recombination at multiple scales. Nature Communications (2017).
4. A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene. Plant Physiology (2024).
5. Delineation of loci governing an extra‐earliness trait in lentil (Lens culinaris Medik.) using the QTL‐Seq approach. Plant Biotechnology Journal (2024).
6. On the estimation of genome-average recombination rates. Genetics (2024).