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Designations for individual genomes and chromosomes in Gossypium

Journal of Cotton Research20181:3

https://doi.org/10.1186/s42397-018-0002-1

Received: 24 April 2018

Accepted: 28 May 2018

Published: 29 June 2018

Abstract

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.

Keywords

NomenclatureIndividual genomeIndividual chromosome Gossypium

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.

As shown in Table 1, the genus is divided into 8 diploid genome groups (A through G, and K), as well as one allopolyploid clade (AD genome) formed from ancient merger and chromosome doubling from A and D genome ancestors. These genome groups were initially defined based on comparative chromosome sizes and chromosome behavior in interspecific hybrids (Beasley 1942; Stephens 1947; Phillips 1966; Fryxell 1992; Endrizzi et al. 1985). Subsequent phylogenetic work (reviewed in Wendel and Grover 2015) has confirmed that each of these genome groups is monophyletic; that is, they have a single origin, with each genome group comprising a natural set of more or less closely related species. Genome groups vary widely in species diversity, from consisting of only a single species (F genome) to larger genome groups containing more than a dozen species each (D, K). The important allopolyploid clade, which includes G. hirsutum and G. barbadense, contains 7 species, including two described only in the last 10 years (G. ekmanianum, G. stephensii) (Krapovickas and Seijo 2008; Gallagher et al. 2017).
Table 1

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

Genome group

Number of species

Species presently recognized

Geographic distribution

A

2

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

B

3–4

G. anomalum, G. triphyllum, G. capitis-viridis, (G. trifurcatum)

Africa, Cape Verde Islands

C

2

G. sturtianum, G. robinsonii

Central and Western Australia

D

13–14

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

E

5–9

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

F

1

G. longicalyx

Endemic to East Africa

G

3

G. bickii, G. australe, G. nelsonii

Central Australia

K

12

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

AD

7

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

Many Gossypium species are taxonomically well-understood, whereas others are poorly known and not well-established as bona fide species; these are indicated with parentheses in Table 1. Most notable in this respect are species or putative species from the horn of Africa and the Arabian Peninsula; several of these species are poorly represented in herbarium collections and no living material has been available for study (last five in Table 2). Remarkably, new species remain to be discovered and or taxonomically described, as evidenced by the recent publication of G. anapoides (Stewart et al. 2014) and G. stephensii (Gallagher et al. 2017). Also notable is the relatively poorly understood diversity in the Mexican arborescent clade, in which additional species likely remain to be described (Wendel and Grover 2015; Feng et al. 2011). More species might be discovered in Australia and in Southern America with new exploitation.
Table 2

Nomenclature of individual genomes and chromosomes for each species in Gossypium, with Chinese translation of species names

Species names

Individual genomea

Individual chromosome

Scientific names

Chinese translations

G. hirsutum Linnaeus

陆地棉

(AD)1

Ah01-Ah13; Dh01-Dh13

G. barbadense Linnaeus

海岛棉

(AD)2

Ab01-Ab13; Db01-Db13

G. tomentosum Nuttall ex Seemann

毛棉

(AD)3

Att01-Att13; Dtt01-Dtt13

G. mustelinum Miers ex Watt

黄褐棉

(AD)4

Am01-Am13; Dm01-Dm13

G. darwinii Watt

达尔文氏棉

(AD)5

Ad01-Ad13; Dd01-Dd13

G. ekmanianum Wittmack

艾克棉

(AD)6

Ae01-Ae13; De01-De13

G. stephensii J. Gallagher, C. Grover & Wendel

斯蒂芬氏棉

(AD)7

As01-As13; Ds01-Ds13

G. herbaceum Linnaeus

草棉

A1

A101-A113

G. herbaceum subs. africanum Hutchinson

阿非利加棉

A1-a

A1a01-A1a13

G. arboreum Linnaeus

亚洲棉

A2

A201-A213

G. anomalum Wawra & Peyritsch

异常棉

B1

B101-B113

G. triphyllum (Harvey & Sonder) Hochreutiner

三叶棉

B2

B201-B213

G. capitis-viridis Mauer

绿顶棉

B3

B301-B313

G. sturtianum Willis

斯特提棉

C1

C101-C113

G. sturtianum var nandewarense Derera

南岱华棉

C1-n

C1n01-C1n13

G. robinsonii Mueller

鲁滨逊氏棉

C2

C201-C213

G. thurberi Todaro

瑟伯氏棉

D1

D101-D113

G. armourianum Kearney

辣根棉

D2–1

D2a01-D2a13

G. harknessii Brandegee

哈克尼西棉

D2–2

D2h01-D2h13

G. davidsonii Kellogg

戴维逊氏棉

D3-d

D3d01-D3d13

G. klotzschianum Andersson

克劳茨基棉

D3-k

D3k01-D3k13

G. aridum (Rose & Standley) Skovsted

旱地棉

D4

D401-D413

G. raimondii Ulbrich

雷蒙德氏棉

D5

D501-D513

G. gossypioides (Ulbrich) Standley

拟似棉

D6

D601-D613

G. lobatum Gentry

裂片棉

D7

D701-D713

G. trilobum (DC.) Skovsted

三裂棉

D8

D801-D813

G. laxum Phillips

松散棉

D9

D901-D913

G. turneri Fryxell

特纳氏棉

D10

D1001-D1013

G. schwendimanii Fryxell & Koch

施温迪茫棉

D11

D1101-D1113

G. sp.nov.

(待命名)

D12

D1201-D1213

G. stocksii Masters in Hooker

司笃克氏棉

E1

E101-E113

G. somalense (Gurke) Hutchinson

索马里棉

E2

E201-E213

G. areysianum Deflers

亚雷西亚棉

E3

E301-E313

G. incanum (Schwartz) Hillcoat

灰白棉

E4

E401-E413

G. longicalyx Hutchinson & Lee

长萼棉

F1

F101-F113

G. bickii Prokhanov

比克氏棉

G1

G101-G113

G. australe Mueller

澳洲棉

G2

G201-G213

G. nelsonii Fryxell

奈尔逊氏棉

G3

G301-G313

G. exiguum Fryxell, Craven & Stewart

小小棉

K1

K101-K113

G. rotundifolium Fryxell, Craven & Stewart

圆叶棉

K2

K201-K213

G. populifolium (Bentham) Mueller ex Todaro

杨叶棉

K3

K301-K313

G. pilosum Fryxell

稀毛棉

K4

K401-K413

G. marchantii Fryxell, Craven & Stewart

马全特氏棉

K5

K501-K513

G. londonderriense Fryxell, Craven & Stewart

伦敦德里棉

K6

K601-K613

G. enthyle Fryxell, Craven & Stewart

林地棉

K7

K701-K713

G. costulatum Todaro

皱壳棉

K8

K801-K813

G. cunninghamii Todaro

肯宁汉氏棉

K9

K901-K913

G. pulchellum (Gardner) Fryxell

小丽棉

K10

K1001-K1013

G. nobile Fryxell, Craven & Stewart

显贵棉

K11

K1101-K1113

G. anapoides Stewart, Craven & Wendel

孪生叶面棉

K12

K1201-K1213

G. anomalum subsp. senarense (Wawra & Peyritsch) Vollesen

桑纳氏棉

B

These species are excluded as they are poorly represented in herbarium collections and no living material has been available for study.

G. trifurcatum Vollesen

三叉棉

E / B

G. vollesenii Fryxell

佛伦生氏棉

E

G. benadirense Mattei

伯纳迪氏棉

E

G. bricchettii (Ulbrich) Vollesen

伯里切特氏棉

E

aSome designations for individual genomes were discussed with James McD Stewart (deceased) in 2007

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.

Declarations

Acknowledgements

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.

Funding

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.

Authors’ contributions

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.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Authors’ Affiliations

(1)
State Key Laboratory of Cotton Biology (China) / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
(2)
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA
(3)
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China

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© The Author(s) 2018

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