Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants

Abstract

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Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

“…While this is a powerful method, it can be limiting if the parents are not available or are unknown [17]. A solution for this is the sequencing of a few gamete genomes (derived from the focal individual), which is sufficient for the inference of genome-wide haplotypes, but relies on existing long-contiguity reference sequences [18][19][20][21].…”

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

“…While this is a powerful method, it can be limiting if the parents are not available or unknown 7 . A solution for this is the sequencing of a few gamete genomes (derived from the focal individual), which is sufficient for the inference of genome-wide haplotypes, but relies on existing long-contiguity reference sequences 8,9,10,11 .…”

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

“…The allelic frequency of bins was around 0.5 and no obvious segregation distortion was detected (Figure 2(a)). Interestingly, distinct from species like maize (Li et al ., 2015; Luo et al ., 2019) and pear ( Pyrus bretschneideri Rehd ) (Shi et al ., 2019), COs were more frequently located on the end of chromosomes and no specific chromosomal distribution pattern of COs was detected in the tea plant (Figure 2(a)).…”

“…A key step of our phasing method was calculating the genetic distance between every pair of bins primarily identified by the Hapi package. This concept was similar to a recent single cell‐based phasing strategy in pear termed ‘barcoding’ (Shi et al ., 2019). However, only 12 single pollens were sequenced therein, rendering it difficult to identify potential errors in assembly (Shi et al ., 2019).…”

“…Single gamete sequencing was demonstrated to be a powerful method to phase genomes, dissect meiotic crossover (CO) patterns or even investigate haploid diversities (Wang et al ., 2012; Lu et al ., 2012b; Hou et al ., 2013; Kirkness et al ., 2013; Li et al ., 2015; Luo et al ., 2019; Nkhoma et al ., 2020). Moreover, the combination of single gamete sequencing with BAC clones or long reads sequencing can be applied for haplotype assembly (Shi et al ., 2019; Campoy et al ., 2020) and this can be streamlined using the R package Hapi (Li et al ., 2018). Another recently developed method combining linked‐read sequencing with pooled pollens used only one DNA library to perform CO detection and haplotype phasing (Sun et al ., 2019).…”