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Keywords:

Gossypium raimondii, Gossypium turneri, cotton

Abstract

(~250 words)

Introduction

(no more than 500 words; must include rationale for the organism/strain)
In 2012, the first reference quality cotton genome was brought to fruition through a monumental, collaborative effort using a combination of next-generation sequencing technologies and targeted Sanger sequencing (Paterson et al, 2012). Gossypium raimondii, a Mesoamerican diploid species, was selected to represent the cotton genus for its small genome size and its relationship to the domesticated polyploid species (Chen et al. Plant Physiol. 2007 Dec; 145(4): 1303–1310). Subsequently, this genome has been widely used by the cotton research community, garnering ~500 citations from a wide spectrum of research. While this genome has been a reliable resource for over 7 years, the advent of third generation 3C (chromatin capture) sequencing technologies provides the ability to increase accuracy in critical genomes by physically associating sequences of greater distance. 
The justification for the original G. raimondii sequence, i.e., its phylogenetic relatedness to the domesticated allopolyploid species and the recruitment of genetic factors from that subgenome during domestication, make G. raimondii and its close relatives potential genetic sources for cotton breeding. Gturneri is species closely related to G. raimondii found in Sonora, Mexico (Fryxell 1978,   Madroño, Vol. 25, No. 3, pp. 155-159). Like G. raimondii, fiber from G. turneri is unspinnable; however, Gturneri has phenotypic characters with agronomic potential, e.g., caducous bracts, insect resistance, and abiotic stress tolerance (https://link.springer.com/article/10.1007/s10681-018-2118-2; DOI: 10.5772/58387 ).  These two species are generally similar, with both having n=13 and relatively small genome sizes (841 Mbp versus 880 Mbp in G. turneri and Graimondii, respectively); however, the species are genetically distinct (Fst=0.76 by SSRs) (  dx.doi.org/10.1139/cjb-2012-0192   ) and a previously published draft genome suggests that gene gain and loss may be elevated in this species (Grover 2018).
Here we describe two de novo generated genomes, G. raimondii (D5) and G. tuneri (D10), which were assembled using newly generated PacBio, Hi-C, and Bionano (G. raimondii only) technologies. The G. raimondii genome sequence reported here represents an independent effort and identifies three significant assembly errors in the initial publication of Graimondii, including a large assembly artifact on the original chromosome 1. We also report a high-quality sequence for the related species, Gturneri, that is suitable for various comparative, genetic, and genomic analyses. Together, these genomes represents a major resource for cotton breeding and for comparative genomics in general.