CottonGen LiftOn Genome Annotations

Overview
Analysis NameCottonGen LiftOn Genome Annotations
MethodLiftOn (v1.0.9)
Sourcecottongen LiftOn
Date performed2026-07-16

LiftOn Genome Annotations

Select a target reference genome section below to download finalized GFF3 annotation files, access the comprehensive pipeline directories (.tar.gz), or interactively explore active alignments via JBrowse 2.

Gene models were mapped using LiftOn, a homology-based pipeline that integrates dual DNA and protein alignments to optimize structural annotation accuracy and preserve open reading frames.

Citation:
Chao, K. H., Heinz, J. M., Hoh, C., Mao, A., Shumate, A., Pertea, M., & Salzberg, S. L. (2025). Combining DNA and protein alignments to improve genome annotation with LiftOn. Genome Research, 35(2), 311-325. doi:10.1101/gr.279620.124

Reference Genome: Gossypium herbaceum  (GosHerb-A1 WHU v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
A1_wagad_USDA_v1 JBrowse 1 Migration 39,100 38,880 99.4% Download GFF3 Download (.tar.gz) Summary
A1_wild_HAU_v1 JBrowse 1 Migration 41,949 41,773 99.6% Download GFF3 Download (.tar.gz) Summary
A1_ZC1_HAU_v1 JBrowse 1 Migration 41,642 41,420 99.5% Download GFF3 Download (.tar.gz) Summary
Reference Genome: Gossypium arboreum (GosArbo-A2 WHU v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
A2_CRI_v1 JBrowse 1 Migration 40,960 40,186 98.1% Download GFF3 Download (.tar.gz) Summary
A2_HAU_v1 JBrowse 1 Migration 41,778 41,502 99.3% Download GFF3 Download (.tar.gz) Summary
A2_HAU_v2 JBrowse 1 Migration 50,210 49,803 99.2% Download GFF3 Download (.tar.gz) Summary
A2_HAU_v2 JBrowse 1 Migration 3,248 2,789 85.9% Download GFF3 Download (.tar.gz) Summary
A2_ZB1_ZSTU_v1 JBrowse 1 Migration 48,236 47,329 98.1% Download GFF3 Download (.tar.gz) Summary
Reference Genome: Gossypium hirsutum  (GosHirs-AD1 TM1 NAU-NBI v1.1) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
AD1_B713_NSF_v1 JBrowse 1 Migration 82,291 75,261 91.5% Download GFF3 Download (.tar.gz) Summary
AD1_Bar32_NSF_v1 JBrowse 1 Migration 75,988 68,981 90.8% Download GFF3 Download (.tar.gz) Summary
AD1_CSX8308_HGS_v1.1 JBrowse 1 Migration 75,767 69,067 91.2% Download GFF3 Download (.tar.gz) Summary
AD1_EM22_HAU_v1 JBrowse 1 Migration 76,102 70,333 92.4% Download GFF3 Download (.tar.gz) Summary
AD1_HPF17_ZJU_v1 JBrowse 1 Migration 79,146 68,274 86.3% Download GFF3 Download (.tar.gz) Summary
AD1_Jin668_HAU_v1 JBrowse 1 Migration 74,637 68,308 91.5% Download GFF3 Download (.tar.gz) Summary
AD1_NDM8_HEAU_v1 JBrowse 1 Migration 80,124 73,777 92.1% Download GFF3 Download (.tar.gz) Summary
AD1_PSC355_USDA_v1 JBrowse 1 Migration 75,746 69,600 91.9% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_HAU2_v2 JBrowse 1 Migration 77,782 71,092 91.4% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_T2T_JZU_v1 JBrowse 1 Migration 79,642 73,632 92.5% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_UTX_v3.1 JBrowse 1 Migration 75,854 69,314 91.4% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_WHU_v1 JBrowse 1 Migration 74,350 68,375 92.0% Download GFF3 Download (.tar.gz) Summary
AD1_TX1000_CRI-JBM_v1 JBrowse 1 Migration 74,520 67,501 90.6% Download GFF3 Download (.tar.gz) Summary
AD1_TX2094_ISU_v2.0 New Assembly (July 2026) 85,371 78,506 92.0% Download GFF3 Download (.tar.gz) Summary
AD1_TX2094_JGI_v1.1 New Assembly (July 2026) 70,768 64,146 90.6% Download GFF3 Download (.tar.gz) Summary
AD1_TX31_HAU_v1 JBrowse 1 Migration 74,092 67,322 90.9% Download GFF3 Download (.tar.gz) Summary
AD1_UA48_HGS_v1.1 JBrowse 1 Migration 77,237 69,727 90.3% Download GFF3 Download (.tar.gz) Summary
AD1_UGA230_HGS_v1.1 JBrowse 1 Migration 75,545 68,979 91.3% Download GFF3 Download (.tar.gz) Summary
AD1_YM11_XAAS_v1 JBrowse 1 Migration 84,720 72,068 85.1% Download GFF3 Download (.tar.gz) Summary
AD1_YZ1_HAU_v1 JBrowse 1 Migration 73,959 65,603 88.7% Download GFF3 Download (.tar.gz) Summary
AD1_ZM113_CRI_v1 JBrowse 1 Migration 78,467 71,427 91.0% Download GFF3 Download (.tar.gz) Summary
AD1_ZM24_CRI_v1 JBrowse 1 Migration 99,706 91,885 92.2% Download GFF3 Download (.tar.gz) Summary
Reference Genome: Gossypium hirsutum  (GosHirs-AD1 TM1 UTX v2.1) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
AD1_B713_NSF_v1 JBrowse 1 Migration 82,291 79,890 97.1% Download GFF3 Download (.tar.gz) Summary
AD1_Bar32_NSF_v1 JBrowse 1 Migration 75,988 73,587 96.8% Download GFF3 Download (.tar.gz) Summary
AD1_CSX8308_HGS_v1.1 JBrowse 1 Migration 75,767 75,128 99.2% Download GFF3 Download (.tar.gz) Summary
AD1_EM22_HAU_v1 JBrowse 1 Migration 76,102 75,405 99.1% Download GFF3 Download (.tar.gz) Summary
AD1_HPF17_ZJU_v1 JBrowse 1 Migration 79,146 74,660 94.3% Download GFF3 Download (.tar.gz) Summary
AD1_Jin668_HAU_v1 JBrowse 1 Migration 74,637 74,220 99.4% Download GFF3 Download (.tar.gz) Summary
AD1_NDM8_HEAU_v1 JBrowse 1 Migration 80,124 79,696 99.5% Download GFF3 Download (.tar.gz) Summary
AD1_PSC355_USDA_v1 JBrowse 1 Migration 75,746 73,845 97.5% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_HAU2_v2 JBrowse 1 Migration 77,782 77,778 100.0% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_T2T_JZU_v1 JBrowse 1 Migration 79,642 79,290 99.6% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_UTX_v3.1 JBrowse 1 Migration 75,854 75,512 99.5% Download GFF3 Download (.tar.gz) Summary
AD1_TM1_WHU_v1 JBrowse 1 Migration 74,350 73,894 99.4% Download GFF3 Download (.tar.gz) Summary
AD1_TX1000_CRI-JBM_v1 JBrowse 1 Migration 74,520 73,480 98.6% Download GFF3 Download (.tar.gz) Summary
AD1_TX2094_ISU_v2.0 New Assembly (July 2026) 85,371 84,029 98.4% Download GFF3 Download (.tar.gz) Summary
AD1_TX2094_JGI_v1.1 New Assembly (July 2026) 70,768 69,982 98.9% Download GFF3 Download (.tar.gz) Summary
AD1_TX31_HAU_v1 JBrowse 1 Migration 74,092 72,827 98.3% Download GFF3 Download (.tar.gz) Summary
AD1_UA48_HGS_v1.1 JBrowse 1 Migration 77,237 75,674 98.0% Download GFF3 Download (.tar.gz) Summary
AD1_UGA230_HGS_v1.1 JBrowse 1 Migration 75,545 75,128 99.4% Download GFF3 Download (.tar.gz) Summary
AD1_YM11_XAAS_v1 JBrowse 1 Migration 84,720 78,909 93.1% Download GFF3 Download (.tar.gz) Summary
AD1_YZ1_HAU_v1 JBrowse 1 Migration 73,959 71,524 96.7% Download GFF3 Download (.tar.gz) Summary
AD1_ZM113_CRI_v1 JBrowse 1 Migration 78,467 77,998 99.4% Download GFF3 Download (.tar.gz) Summary
AD1_ZM24_CRI_v1 JBrowse 1 Migration 99,706 99,261 99.6% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium barbadense (GosBarb-AD2 3-79 HGS v1.1) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
AD2_379_HAU_v3 JBrowse 1 Migration 76,754 76,660 99.9% Download GFF3 Download (.tar.gz) Summary
AD2_H7124_ZJU_v1.1 JBrowse 1 Migration 75,071 75,029 99.9% Download GFF3 Download (.tar.gz) Summary
AD2_M210936_HAU_v1 JBrowse 1 Migration 75,609 72,797 96.3% Download GFF3 Download (.tar.gz) Summary
AD2_P90_HEAU_v1 JBrowse 1 Migration 79,613 79,551 99.9% Download GFF3 Download (.tar.gz) Summary
AD2_Y2003-GB249_HAU_v1 JBrowse 1 Migration 71,549 71,367 99.7% Download GFF3 Download (.tar.gz) Summary
AD2_Y2005-AZB51_HAU_v1 JBrowse 1 Migration 74,094 73,662 99.4% Download GFF3 Download (.tar.gz) Summary
AD2_Y2010-AZB375_HAU_v1 JBrowse 1 Migration 71,963 71,798 99.8% Download GFF3 Download (.tar.gz) Summary
AD2_Y2013-Yuma_HAU_v1 JBrowse 1 Migration 76,046 73,454 96.6% Download GFF3 Download (.tar.gz) Summary
AD2_Y2016-AZK101_HAU_v1 JBrowse 1 Migration 71,312 71,115 99.7% Download GFF3 Download (.tar.gz) Summary
AD2_Y2029-Giza7_HAU_v1 JBrowse 1 Migration 76,012 74,303 97.8% Download GFF3 Download (.tar.gz) Summary
AD2_Y2031-AZB339_HAU_v1 JBrowse 1 Migration 72,247 70,819 98.0% Download GFF3 Download (.tar.gz) Summary
AD2_Y2032-AZB634_HAU_v1 JBrowse 1 Migration 72,870 71,818 98.6% Download GFF3 Download (.tar.gz) Summary
AD2_Y2033-GB660_HAU_v1 JBrowse 1 Migration 72,281 69,894 96.7% Download GFF3 Download (.tar.gz) Summary
AD2_Y2034-GB776_HAU_v1 JBrowse 1 Migration 74,527 73,070 98.0% Download GFF3 Download (.tar.gz) Summary
AD2_Y2036-JunHai1_HAU_v1 JBrowse 1 Migration 75,774 70,943 93.6% Download GFF3 Download (.tar.gz) Summary
AD2_Y3048-CEG_HAU_v1 JBrowse 1 Migration 75,755 73,986 97.7% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium tomentosum (GosTome-AD3 HGS v1.1) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
AD3_HAU_v1 JBrowse 1 Migration 72,648 71,557 98.5% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium anomalum (GosAnom-B1 JAAS v1.2) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
B1_NSF_v1 JBrowse 1 Migration 37,016 36,969 99.9% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium harknessii (GosHark-D2-2_CRI_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D2-2_ISU_v1 JBrowse 1 Migration 25,367 25,099 98.9% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium davidsonii (GosDavi-D3-d_CRI_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D3-d_ISU_v1 JBrowse 1 Migration 30,022 30,022 100.0% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium klotzschianum (GosKlot-D3-k_ISU_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D3-k_CRI_v1 JBrowse 1 Migration 43,254 39,967 92.4% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium raimondii (GosRaim-D5 D502 HAU v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D5_D5-3_PKU_v1 JBrowse 1 Migration 53,167 52,332 98.4% Download GFF3 Download (.tar.gz) Summary
D5_D5-8_ISU_v1 JBrowse 1 Migration 25,090 24,965 99.5% Download GFF3 Download (.tar.gz) Summary
D5_GPD5lz_HAU_v1 JBrowse 1 Migration 42,376 42,300 99.8% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium gossypioides (GosGoss-D6_ISU_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D6_CRI_v1 JBrowse 1 Migration 39,601 35,609 89.9% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium trilobum (GosTril-D8_ISU_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
D8_CRI_v1 JBrowse 1 Migration 28,298 28,297 100.0% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium stocksii (GosStoc-E1_NSF_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
E1_HAU_v1 JBrowse 1 Migration 40,321 40,036 99.3% Download GFF3 Download (.tar.gz) Summary
Reference Genome:  Gossypium longicalyx (GosLong-F1_NSF_v1.0) 🔍 View in JBrowse 2
Target Genome Status / Source Total Genes Lifted Genes Completeness (%) GFF3 Annotation Pipeline Data Run Summary
F1_HAU_v1 JBrowse 1 Migration 41,633 41,305 99.2% Download GFF3 Download (.tar.gz) Summary