Genome Assembly of Finger Lemon 'YaoJi' Reveals Genetic Underpinnings of Rind Color Differences

A research team successfully sequenced and assembled the genome of the purple finger lemon variety 'YaoJi', revealing a genome size of 314.63 Mb across nine chromosomes. The study identified 21,154 protein-coding genes and significant gene expression differences linked to rind color variations. This research presents a high-quality genome sequence, shedding light on the evolutionary history of finger lemons and facilitating future functional gene mining. These findings hold the potential for enhancing variety selection and improving the economic and medicinal value of finger lemons.

Finger lemon (Citrus australasica), valued for its unique flavor and medicinal properties, has an incomplete genome data, especially for the purple variety 'YaoJi'. Current research has focused on its chemical composition, but the genetic basis of rind color variation remains unexplored. The lack of high-quality genome data hampers understanding of its evolution.

A study (DOI: 10.48130/tp-0024-0021) published in Tropical Plants on 21 May 2024, aims to sequence and analyze the 'YaoJi' genome using nanopore technology, investigating the molecular mechanisms underlying rind color differences to inform future selection and cultivation strategies.

In this study, the genome of finger lemon 'YaoJi' was assembled using a whole genome birdshot (WGS) strategy and second-generation sequencing technology. A second-generation small fragment DNA library was constructed, yielding 35.95 Gb of filtered data, with the genome size predicted to be approximately 290.1 Mb using the K-mer method. Nanopore sequencing generated 13.69 Gb of long-read data for ab initio assembly, resulting in a high-quality genome of 313.91 Mb, 175 contigs, and a Contig N50 of 6.64 Mb. The assembled genome was mapped to nine chromosomes, achieving a size of 314.64 Mb and a Scaffold N50 of 32.81 Mb. Quality assessment with BUSCO showed a 98.4% integrity of single-copy homologous genes.The genome annotation identified 21,154 protein-coding genes and 164.7 Mb of repetitive sequences. Phylogenetic analysis revealed finger lemons diverged from sweet orange (Citrus sinensis (L.) Osbeck) and Cremantine red orange (Citrus × clementina) around 10 Mya, with a whole genome duplication event inferred from the Ks distribution. Transcriptome analysis of different rind colors indicated high expression of flavonoid and carotenoid biosynthesis genes and related transcription factors, suggesting these pathways contribute to rind color variation in finger lemons.

According to the study's lead researcher, Zhiqiang Xia, "The purpose of this study is to investigate the molecular mechanism and provide data for the evolutionary genetic pattern, to provide a reference value for the selection and cultivation in the future."

In summary, this study constructed a high-quality reference genome of the finger lemon "YaoJi" by nanopore sequencing and explored the mechanisms underlying the color differences in the rind of finger lemon.These findings provide a genomic foundation for further genetic studies and breeding programs of finger lemon species. Future research will focus on verifying rind color regulation and exploring additional functional genes to enhance finger lemon cultivation and selection.