A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

Abstract

SUMMARYFor diploid organisms that are highly heterozygous, a phased haploid genome can greatly aid in functional genomic, population genetic and breeding studies. Based on the genome sequencing of 135 single sperm cells of the elite tea cultivar ‘Fudingdabai’, we herein phased the genome of Camellia sinensis, one of the most popular beverage crops worldwide. High‐resolution genetic and recombination maps of Fudingdabai were constructed, which revealed that crossover (CO) positions were frequently located in the 5′ and 3′ ends of annotated genes, while CO distributions across the genome were random. The low CO frequency in tea can be explained by strong CO interference, and CO simulation revealed the proportion of interference insensitive CO ranged from 5.2% to 11.7%. We furthermore developed a method to infer the relatedness between tea accessions and detected complex kinship and genetic signatures of 106 tea accessions. Among them, 59 accessions were closely related with Fudingdabai and 31 of them were first‐degree relatives. We additionally identified genes displaying allele specific expression patterns between the two haplotypes of Fudingdabai and genes displaying significantly differential expression levels between Fudingdabai and other haplotypes. These results lay the foundation for further investigation of genetic and epigenetic factors underpinning the regulation of gene expression and provide insights into the evolution of tea plants as well as a valuable genetic resource for future breeding efforts.

Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

“…Even long sequencing reads are generally insufficient for long-range phasing, and auxiliary data types are required. One example is single pollen cell sequencing (Zhang et al 2021), which was recently used for comprehensive haplotype reconstruction in autopolyploid potato (Sun et al 2022). Here, we propose an alternative method in which PacBio HiFi reads of the potato cultivar Altus are combined with cost-effective low-coverage short-read sequences from multiple offspring samples.…”

“…Even long sequencing reads are generally insufficient for long-range phasing, and auxiliary data types are required. One example is single pollen cell sequencing (Zhang et al 2021), which was recently used for comprehensive haplotype reconstruction in autopolyploid potato (Sun et al 2022).…”

Combining novel technologies with interdisciplinary basic research to enhance horticultural crops

“…Among them, single‐cell sequencing of gametes is an ideal method for phasing highly heterozygous horticultural crops. This method has been adopted for some horticultural crops like pear (Shi et al., 2019), apricot ( Prunus armeniaca ) (Campoy et al., 2020), and tea trees (Zhang et al., 2021c), and it provides novel routes for the sequencing of polyploid horticultural crops with complex genomes. Moreover, single‐gamete sequencing also uncovers the landscape of crossover (CO) patterns and thereby allows rapid generation of genetic maps for horticulture crops, many of which are difficult to construct from segregating populations (Campoy et al., 2020; Zhang et al., 2021c).…”

Conservation of an Agrobacterium cT-DNA insert in Camellia section Thea reveals the ancient origin of tea plants from a genetically modified ancestor

“…Because of the economical and cultural importance of the genus Camellia, many efforts have been made to reconstruct its molecular evolution. The complex genetic relations between cultivated tea plants and their wild ancestors have been studied extensively (Prince and Parks, 2001;Wachira et al, 2001;Chen and Yamaguchi, 2002;Xiao and Parks, 2003;Sharma et al, 2009;Vijayan et al, 2009;Sharma et al, 2010;Liu et al, 2012;Yao et al, 2012;Yang et al, 2013;Huang et al, 2014;Zhang et al, 2014;Xu et al, 2015;Meegahakumbura et al, 2016;Yang et al, 2016;Wang et al, 2020;Xia et al, 2020;Zhang et al, 2020b;Wu et al, 2022); Zhang et al, 2020b. Nuclear DNA-based Camellia phylogenies have been proposed on the basis of ribosomal DNA (Vijayan et al, 2009;Xu et al, 2015;Zhang M. et al, 2021), single-nucleotide polymorphisms (SNPs) and restriction-site associated (RAD) markers (Yang et al, 2016), transposons (Yao et al, 2017) and transcript sequences (Zhang et al, 2022;Wu et al, 2022). Recently, whole genome sequencing has provided new opportunities for phylogenetic tree construction (Wei et al, 2018;Wang et al, 2020;Xia et al, 2020;Zhang et al, 2020b;Zhang et al, 2020b;Zhang X. et al, 2021).…”

“…Because of the economical and cultural importance of the genus Camellia , many efforts have been made to reconstruct its molecular evolution. The complex genetic relations between cultivated tea plants and their wild ancestors have been studied extensively ( Prince and Parks, 2001 ; Wachira et al., 2001 ; Chen and Yamaguchi, 2002 ; Xiao and Parks, 2003 ; Sharma et al., 2009 ; Vijayan et al., 2009 ; Sharma et al., 2010 ; Liu et al., 2012 ; Yao et al., 2012 ; Yang et al., 2013 ; Huang et al., 2014 ; Zhang et al., 2014 ; Xu et al., 2015 ; Meegahakumbura et al., 2016 ; Yang et al., 2016 ; Wang et al., 2020 ; Xia et al., 2020 ; Zhang et al., 2020b ; Wu et al., 2022 ); Zhang et al., 2020b .…”