The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

Abstract

Cotton is an important crop that has made significant gains in production over the last century.Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx.This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.

The Gossypium stocksii genome as a novel resource for cotton improvement

“…Over 97% complete BUSCOs were recovered, most of which were single copy (88.9%, versus 8.7% duplicated). The LTR Assembly Index (LAI) (Ou et al 2018) was also within guidelines for “reference-quality” genomes (LAI = 10-20; G. stocksii LAI = 15.4), and dotplots (Figure 1) with existing high-quality cotton genome assemblies (Paterson et al 2012; Du et al 2018; Udall et al 2019a, 2019b; Grover et al 2020; Huang et al 2020) further indicates the high quality nature of this genome.…”

“…Pairwise comparisons of G. stocksii with G. herbaceum (A1; (Huang et al 2020), G. raimondii (D5; (Udall et al 2019a), G. longicalyx (F1; (Grover et al 2020), G. arboreum (A2; (Huang et al 2020), G. turneri (D10; (Udall et al 2019a), and G. australe (G2; (Cai et al 2019). …”

“…Over 97% complete BUSCOs were recovered, most of which were single copy (88.9%, versus 8.7% duplicated). The LTR Assembly Index (LAI) (Ou et al 2018) was also within guidelines for "reference-quality" genomes (LAI = 10-20; G. stocksii LAI = 15.4), and dotplots ( Figure 1 ) with existing high-quality cotton genome assemblies (Paterson et al 2012;Du et al 2018;Udall et al 2019aUdall et al , 2019bGrover et al 2020;Huang et al 2020) further indicates the high quality nature of this genome. Annotation of the G. stocksii genome revealed 37,889 transcripts representing 34,928 unique genes, similar to other cotton diploid genomes (range 37,505 to 43,952; (Paterson et al 2012;Du et al 2018;Udall et al 2019a;Grover et al 2020;Huang et al 2020) .…”

“…Transposable elements were annotated using a combination of RepeatMasker (Smit et al 2015) and "One code to find them all" (Bailly-Bechet et al 2014) . A custom library based off of Repbase 23.04 (Bao et al 2015) combined with cotton-specific repeats (Grover et al 2020) was used in conjunction with RepeatMasker to mark repeats in the genome. Adjacent matches were merged using "One code to find them all," and the output was aggregated and summarized in R/4.0.3 (R Core Team 2017) using dplyr /0.8.1 (Wickham et al 2015) .…”

“…Orthologous relationships between G. stocksii and other diploid cottons were determined via OrthoFinder Kelly 2015, 2019) . Proteins from G. longicalyx (Grover et al 2020) , G. arboreum (Li et al 2014;Du et al 2018;Huang et al 2020) , G. herbaceum (Huang et al 2020) , G. raimondii (Paterson et al 2012;Udall et al 2019a) , G. turneri (Udall et al 2019a) , and G. australe (Cai et al 2019) were downloaded from CottonGen ( https://www.cottongen.org ; (Yu et al 2014) and run using default parameters. Code is available from https://github.com/Wendellab/stocksii .…”