TheGossypium longicalyxgenome as a resource for cotton breeding and evolution

Abstract

40Cotton is an important crop that has made significant gains in production over the last century. 41 Emerging pests such as the reniform nematode have threatened cotton production. The rare 42 African diploid species Gossypium longicalyx is a wild species that has been used as an 43 important source of reniform nematode immunity. While mapping and breeding efforts have 44 made some strides in transferring this immunity to the cultivated polyploid species, the 45 complexities of interploidal transfer combined with substantial linkage drag have inhibited 46 progress in this area. Moreover, this species shares its most recent common ancestor with the 47 cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, 48 spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. 49This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C 50 chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level 51 assembly. The utility of the G. longicalyx genome for understanding reniform immunity and 52 fiber evolution is discussed. 53 54 55 73 species exhibit degrees of resistance, only G. longicalyx exhibits immunity to infection (Yik and 74 Birchfield 1984). This is significant as reniform nematode has emerged as a major source of 75 cotton crop damage, reducing cotton production by over 205 million bales per year (Lawrence et 76 al. 2015) and accounting for ~11% of the loss attributable to pests (Khanal et al. 2018). Current 77 reniform resistant lines are derived from complex breeding schemes which are required to 78 introgress reniform immunity from the diploid G. longicalyx into polyploid G. hirsutum (Bell 79 and Robinson 2004; Dighe et al. 2009; Khanal et al. 2018); however, undesirable traits have 80 3 accompanied this introgression (Nichols et al. 2010) extreme stunting of seedlings and plants 81 exposed to dense nematode populations, prohibiting commercial deployment (Zheng et al. 2016). 83The genome of G. longicalyx is also valuable because it is phylogenetically sister to the only 84 diploid clade with spinnable fiber (Wendel and Albert, 1992; Wendel and Grover, 2015; Chen et 85 al., 2016), the A-genome species, which contributed the maternal ancestor to polyploid cotton. 86 Consequently, there has been interest in this species as the ancestor to spinnable fiber (Hovav et 87 al. 2008; Paterson et al. 2012), although progress has been limited due to lack of genomic 88 resources in G. longicalyx. Comparisons between the G. longicalyx genome and other cotton 89 genomes, including the domesticated diploids (Du et al. 2018), may provide clues into the 90 evolutionary origin of "long" fiber. 92Here we describe a high-quality, de novo genome sequence for G. longicalyx, a valuable 93 resource for understanding nematode immunity in cotton and possibly other species. This 94 genome also provides a foundation to understand the evolutionary origin of spinnable fiber in 95 Gossypium. 96 97 98

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

“…(1.20%) or missing (2.30%), indicating a general completeness of the genome. This BUSCO recovery is similar to recent publications of other diploid cotton genomes (Huang et al, 2020, Grover et al, 2020Grover et al, 2021. Annotation of the genome produced 39,100 unique genes, similar to the previously published cotton diploids (Paterson et al 2012;Li et al 2014;Du et al 2018;Udall et al 2019;Grover et al 2020Grover et al , 2021cGrover et al , 2021bHuang et al 2020).…”

“…This BUSCO recovery is similar to recent publications of other diploid cotton genomes (Huang et al, 2020, Grover et al, 2020Grover et al, 2021. Annotation of the genome produced 39,100 unique genes, similar to the previously published cotton diploids (Paterson et al 2012;Li et al 2014;Du et al 2018;Udall et al 2019;Grover et al 2020Grover et al , 2021cGrover et al , 2021bHuang et al 2020). The annotation of A1-Wagad contained ~5000 fewer unique genes than the published annotation for A1-africanum, possibly due to annotation methods and/or filtering.…”

“…2020), A1-073, (Page et al 2013), and A1-155 (Page et al 2013). These were aligned to the outgroup reference genome G. longicalyx (Grover et al . 2020) using BWA (Li and Durbin 2009) with default arguments.…”

“…To observe syntenic conservation, whole-genome alignments were generated between wagad and africanum using Mummer (Marçais et al 2018). Alignments were visualized using dotPlotly Because fiber is one of the primary agronomic traits of interest, we screened the remaining wagad-unique nonsynonymous genes by their associated GO, Interpro, and Panther functional annotation (Grover et al 2020) were considered differentially expressed.…”

“…https://github.com/tpoorten/dotPlotly) in R (version 3.6.0) (R Development Core Team and Others 2011) to identify regions with major structural variations.Illumina DNA reads were generated and/or downloaded for A1-Wagad (PRJNA421172) and several accessions of G. herbaceum subspecies africanum, including accession 'Mutema'(Huang et al 2020), A1-073, (Page et al 2013), and A1-155 (Page et al 2013. These were aligned to the outgroup reference genome G. longicalyx(Grover et al 2020) using BWA(Li and Durbin 2009) with default arguments. Single nucleotide polymorphisms (SNPs) and small insertion-deletion polymorphisms (INDELs) were identified using the Sention(Kendig et al 2019) DNAseq workflow and filtered to remove sites with >90% missing data or more than two alleles.The resulting SNPs among A1-africanum, A1-073, A1-155, and A1-Wagad were annotated with SnpEff(Cingolani et al 2012b).…”