About Genomics

Genomics

We collected 25 genome assemblies of 16 germplasms including the diploids A1-, A2-, D1-, D5-, D10-genomes and allopolyploids AD1-, AD2-, AD3-, AD4- and AD5-genomes^[1-14]. By genome alignment, genomic synteny was constructed. We collected 1,521,966 genes of 25 genome assemblies and constructed gene index of 25 genome assemblies at the pangenome level. Three main functions can be performed in Genomics module, including Genome synteny, gene index and gene search.

Genome synteny

Genomic synteny was constructed based on genome alignment using Mummer. User can browse genome alignment by Dotplot at global level; User can also browse local alignment by GBrowser.

Gene index

1,521,966 genes of 25 genome assemblies were used to construct the gene index. Gene synteny of every pairs from 25 genome assemblies were detected by McScanX. Finally, 146,881 gene clusters were identified as the gene index of cotton. All gene indexes were functionally annotated based on the with homology with A. thaliana.The gene clusters with the same A. thaliana gene were merged. User can search the interested gene index and browse syntenic genes and their functions by inputting gene ID.

Gene search

1,521,966 genes of 25 genome assemblies were included in CottonMD. All genes were functionally annotated based on their homologies with the genes in A. thaliana. User can search the functions of interested genes by inputting gene ID.

Genome ID	Genome group	Germplasm	Species	Genome size	Predicted gene number
A1_WHU	A1	Mutema	Gossypium herbaceum	1,556,086,907	43,952
A2_BGI	A2	SXY1	Gossypium arboreum	1,694,649,772	40,134
A2_CRI	A2	SXY1	Gossypium arboreum	1,710,104,083	40,960
A2_HAU	A2	SXY1	Gossypium arboreum	1,621,030,562	41,778
A2_WHU	A2	SXY1	Gossypium arboreum	1,636,985,834	40,134
D1_ISU	D1	D1-35	Gossypium thurberi	496,766,117	31,520
D5_HAU	D5	D502	Gossypium raimondii	750,205,487	40,820
D5_JGI	D5	D5	Gossypium raimondii	761,406,121	77,267
D5_NSF	D5	D5-4	Gossypium raimondii	734,884,094	41,030
D10_NSF	D10	D10-3	Gossypium turneri	755,203,240	39,692
TM1_HAU	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,281,853,441	115,835
TM1_ZJU	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,298,437,019	72,761
TM1_CRI	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,287,866,413	79,703
TM1_NBI	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,546,077,166	70,478
TM1_WHU	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,290,427,971	74,350
TM1_UTX	AD1	Texas Marker 1 (TM-1)	Gossypium hirsutum	2,305,241,538	107,216
ZM24 CRI	AD1	ZM24	Gossypium hirsutum	2,308,215,698	99,706
HEBAU_NDM8	AD1	NDM8	Gossypium hirsutum	2,291,769,868	80,123
3-79_HAU	AD2	3-79	Gossypium barbadense	2,266,746,731	109,778
3-79_HGS	AD2	3-79	Gossypium barbadense	2,195,804,943	108,363
H7124_ZJU	AD2	Hai7124 (H7124)	Gossypium barbadense	2,226,679,100	75,071
P90_HEBAU	AD2	Pima90	Gossypium barbadense	2,210,138,243	79,613
AD3_HGS	AD3	7179.01,02,03	Gossypium tomentosum	2,193,557,323	112,713
AD4_JGI	AD4	1408120.09, 1408120.10, 1408121.01, 1408121.02, 1408121.03	Gossypium mustelinum	2,315,094,184	106,487
AD5_HGS	AD5	AD5-32, no. 1808015.09	Gossypium darwinii	2,182,957,963	97,407

References

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[2]	Du X, Huang G, He S, et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits[J]. Nature Genetics, 2018.
[3]	Grover C E, Arick M A, Adam T, et al. Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing[J]. Genome Biology and Evolution, 2018 (1):1.
[4]	Udall J A, Long E, Hanson C, et al. De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri[J]. G3: Genes\|Genomes\|Genetics, 2019, 9 (10).
[5]	Chen Z J, Sreedasyam A, Ando A, et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement[J]. Nature Genetics, 2020, 52 (5).
[6]	Yang Z, Ge X, Yang Z, et al. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars[J]. Nature Communications, 2019, 10 (1).
[7]	Hu Y, J Chen, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature Genetics, 2019.
[8]	Wang M, Tu L, Yuan D, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense[J]. Nature Genetics, 2019.
[9]	D Yuan, Z Tang, M Wang,et al. OPEN The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights[J]. Sci Rep. 2015 Dec 4;5:17662.
[10]	Ma Z, Zhang Y, Wu L, et al. High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement[J]. Nature Genetics, 2021: 1-7.
[11]	Li F, Fan G, Wang K, et al. Genome sequence of the cultivated cotton Gossypium arboreum[J]. Nature genetics, 2014, 46(6): 567-572.
[12]	Wang M, Li J, Wang P, et al. Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton[J]. Mol.
[13]	Paterson A H, Wendel J F, Gundlach H, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres[J]. Nature, 2012, 492(7429): 423-427.
[14]	Zhang T, Hu Y, Jiang W, et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement[J]. Nature biotechnology, 2015, 33(5): 531-537.

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