- Open Access
Designations for individual genomes and chromosomes in Gossypium
© The Author(s) 2018
- Received: 24 April 2018
- Accepted: 28 May 2018
- Published: 29 June 2018
Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.
- Individual genome
- Individual chromosome
Because of its diversity and economic significance, the cotton genus (Gossypium) has been subjected to decades of taxonomic, cytogenetic, and phylogenetic analyses. Accordingly, a reasonably well-documented phylogenetic and taxonomic understanding has developed, as recently summarized (Wendel and Grover 2015). Work published since that time also supports the emerging picture of species relationships and diversification (Grover et al. 2015a, 2015b; Chen et al. 2016; Gallagher et al. 2017). Our purpose here is to provide a brief summary of this understanding, and to introduce the chromosomal context for the genome designations that are widely used by cotton researchers worldwide.
Taxonomic, cytogenetic and geographic diversity of species of Gossypium. Included are descriptions are each genome group and the collective geographic distribution of the included species. Genomic placements and taxonomic status of species enclosed by parentheses remain to be established as they are poorly known
Number of species
Species presently recognized
G. arboreum, G. herbaceum
Wild forms known only from Southern Africa, but with an indigenous domesticated range encompassing parts of Africa, the middle east, and Asia
G. anomalum, G. triphyllum, G. capitis-viridis, (G. trifurcatum)
Africa, Cape Verde Islands
G. sturtianum, G. robinsonii
Central and Western Australia
G. thurberi, G. armourianum, G. harknessii, G. davidsonii, G. klotzschianum, G. aridum, G. raimondii, G. gossypioides, G. lobatum, G. trilobum, G. laxum, G. turneri, G. schwendimanii, (G. sp.nov.)
Primarily Mexico, with range extensions into Peru, the Galapagos Islands, and southern Arizona
G. stocksii, G. somalense, G. areysianum, G. incanum, G. trifurcatum, (G. benidirense), (G. bricchettii), (G. vollesenii), (G. trifurcatum)
Poorly understood native ranges of many species, but collectively in parts of the Arabian Peninsula, Northeast Africa, and Southwest Asia
Endemic to East Africa
G. bickii, G. australe, G. nelsonii
G. anapoides, G. costulatum, G. cunninghamii, G. enthyle, G. exiguum, G. londonderriense, G. marchantii, G. nobile, G. pilosum, G. populifolium, G. pulchellum, G. rotundifolium
Northwest Australia, Cobourg Peninsula, Northern Territory, Australia
G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum, G. darwinii, G. ekmanianum, G. stephensii
Wild species are from the New World tropics and subtropics, including Hawaii, NE Brazil, the Dominican Republic, and the Galapagos Islands. A recently described species (G. stephensii) is from the Wake Atoll near French Polynesia. The indigenous cultivated range of the two domesticated species G. barbadense and G. hirsutum encompasses many parts of the drier New World tropics and subtropics, with overlapping ranges in the Caribbean and elsewhere
Nomenclature of individual genomes and chromosomes for each species in Gossypium, with Chinese translation of species names
G. hirsutum Linnaeus
G. barbadense Linnaeus
G. tomentosum Nuttall ex Seemann
G. mustelinum Miers ex Watt
G. darwinii Watt
G. ekmanianum Wittmack
G. stephensii J. Gallagher, C. Grover & Wendel
G. herbaceum Linnaeus
G. herbaceum subs. africanum Hutchinson
G. arboreum Linnaeus
G. anomalum Wawra & Peyritsch
G. triphyllum (Harvey & Sonder) Hochreutiner
G. capitis-viridis Mauer
G. sturtianum Willis
G. sturtianum var nandewarense Derera
G. robinsonii Mueller
G. thurberi Todaro
G. armourianum Kearney
G. harknessii Brandegee
G. davidsonii Kellogg
G. klotzschianum Andersson
G. aridum (Rose & Standley) Skovsted
G. raimondii Ulbrich
G. gossypioides (Ulbrich) Standley
G. lobatum Gentry
G. trilobum (DC.) Skovsted
G. laxum Phillips
G. turneri Fryxell
G. schwendimanii Fryxell & Koch
G. stocksii Masters in Hooker
G. somalense (Gurke) Hutchinson
G. areysianum Deflers
G. incanum (Schwartz) Hillcoat
G. longicalyx Hutchinson & Lee
G. bickii Prokhanov
G. australe Mueller
G. nelsonii Fryxell
G. exiguum Fryxell, Craven & Stewart
G. rotundifolium Fryxell, Craven & Stewart
G. populifolium (Bentham) Mueller ex Todaro
G. pilosum Fryxell
G. marchantii Fryxell, Craven & Stewart
G. londonderriense Fryxell, Craven & Stewart
G. enthyle Fryxell, Craven & Stewart
G. costulatum Todaro
G. cunninghamii Todaro
G. pulchellum (Gardner) Fryxell
G. nobile Fryxell, Craven & Stewart
G. anapoides Stewart, Craven & Wendel
G. anomalum subsp. senarense (Wawra & Peyritsch) Vollesen
These species are excluded as they are poorly represented in herbarium collections and no living material has been available for study.
G. trifurcatum Vollesen
E / B
G. vollesenii Fryxell
G. benadirense Mattei
G. bricchettii (Ulbrich) Vollesen
This taxonomic framework provides a justification for a nomenclature for individual genomes and chromosomes in each species in Gossypium. A stable and accepted nomenclature will facilitate comparisons among the many kinds of studies that might be conducted in Gossypium, which range from basic taxonomic exploration to breeding and germplasm introgression. As shown in Table 2, designations of genomes and chromosomes in each species, subspecies and variety in Gossypium are suggested, including for G. herbaceum subs. africanum with its genome as A1-a, which might be useful for ongoing genomic studies, and one Mexican arborescent species with a genome designated as D12, as this species may soon be described as a new D genome species. The last five species in Table 2 have not been assigned genome designations because they are poorly represented in herbarium collections and no living material has been available for study.
A comparative nomenclature of individual chromosomes in Gossypium is facilitated by the many early studies in the later decades of the previous century, when cotton karyotype studies were frequently conducted (Edwards 1977, 1979a, 1979b; Wang et al. 1994; Endrizzi et al. 1985; Wendel and Grover 2015). These earlier investigations provided an important foundation for the transition into the molecular biology era. By using cultivars or wild species in Gossypium, there were increasingly frequent reports on genetic mapping related to linkage groups (Brubaker et al. 1999; Rong et al. 2004; Khan et al. 2016), on identifications of individual chromosomes (Wang et al. 2007, 2008; Gan et al. 2011, 2012, 2013; Shan et al. 2016), and even on microdissection and microcloning of individual chromosomes (Peng et al. 2012). De novo sequence-based genomic studies provided detailed information on single or pseudo-chromosomes (Wang et al. 2012; Paterson et al. 2012; Li et al. 2014, 2015; Zhang et al. 2015; Liu et al. 2015; Yuan et al. 2015).
These and many other studies collectively indicate that a clear nomenclature of individual chromosomes in Gossypium will be useful to facilitate communication and to provide consistency in chromosome designations. Here we suggest such designations (Table 2) for all clades in Gossypium, with the exception of the last five taxa that are too poorly understood taxonomically and cytogenetically to be included. For the seven allotetraploid species, the first letters of their specific names are used instead of their corresponding genome designations. Ah and Dh stand for corresponding chromosome sets of A-sub and D-sub genome, respectively, for G. hirsutum, as well as Ab and Db for G. barbadense, Att and Dtt for G. tomentosum, Am and Dm for G. mustelinum, Ad and Dd for G. darwinii, Ae and De for G. ekmanianum, and As and Ds for G. stephensii. At and Dt are more broadly used terms that designate chromosomes of A-sub and D-sub genomes in all allotetraploid cottons, respectively, from which the Att and Dtt for G. tomentosum are distinguished. Generally, in diploid species, the designations for individual chromosomes correspond to the individual genomes. There is another exception for G. armourianum and G. harknessii because of the historical use of the genome designation D2 for both of these species; accordingly, ‘a’ and ‘h’, the first letters of their specific epithets, are used to clarify this confusion, so that the individual chromosomes of the two species are designated D2a1 - D2a13 and D2h1 ~ D2h13, respectively. The other break with tradition is the simplifying omission of dashes in individual chromosome designations for G. herbaceum subs. africanum, G. sturtianum var nandewarense, G. armourianum, G. harknessii, G. davidsonii and G. klotzschianum.
We thank Dr. James McD Stewart (deceased, serving as a professor in Arkansas State University in 2007) for his some suggestions to the designations for individual genomes in Gossypium.
National Natural Science Foundation of China (31530053).
Availability of data and materials
Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
Wang KB conceived of the subject, and participated in its design and coordination and jointly to draft the manuscript; Wendel JF participated in the design and jointly to draft the manuscript; Hua JP participated in the design and helped to draft the manuscript. All authors read and approved the final manuscript.
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