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Genes with DMLs - Summary Report
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Genes with DMLs - Summary Report

Overview

This report provides a comprehensive list of genes that contain Differentially Methylated Loci (DMLs) in the Chilean mussel (Mytilus chilensis) genome.

Summary Statistics

  • Total unique genes with DMLs: 159
  • Total DML-gene associations: 224
  • Chromosomes covered: 13 out of 14 (Chromosome_9 excluded due to GFF3 typo)

Distribution by Chromosome

Chromosome Number of Genes Percentage
Chromosome_3 34 21.4%
Chromosome_6 30 18.9%
Chromosome_1 25 15.7%
Chromosome_11 25 15.7%
Chromosome_8 24 15.1%
Chromosome_2 16 10.1%
Chromosome_4 16 10.1%
Chromosome_14 14 8.8%
Chromosome_5 13 8.2%
Chromosome_12 12 7.5%
Chromosome_13 6 3.8%
Chromosome_10 5 3.1%
Chromosome_7 4 2.5%

Complete List of Genes with DMLs

Chromosome_1 (25 genes)

  1. MCH000014.1 (260,795-262,480) - +38.0% methylation
  2. MCH000116.1 (6,006,721-6,011,468) - +31.6% methylation
  3. MCH000252.1 (14,103,829-14,119,218) - +25.5% and -43.5% methylation
  4. MCH000377.1 (19,413,325-19,422,450) - +38.7% methylation
  5. MCH000500.1 (28,305,600-28,339,195) - -36.7% methylation
  6. MCH000594.1 (32,271,440-32,275,612) - +26.6% methylation
  7. MCH000785.1 (41,820,576-41,828,388) - -49.5% methylation
  8. MCH000868.1 (45,733,583-45,793,090) - +44.1% methylation
  9. MCH000891.1 (47,134,964-47,150,994) - +48.0% methylation
  10. MCH000976.1 (52,244,221-52,269,016) - -38.5% methylation
  11. MCH000977.1 (52,271,699-52,294,742) - +37.9% methylation
  12. MCH000993.1 (53,157,139-53,181,473) - +66.9% methylation
  13. MCH001009.1 (53,522,130-53,542,611) - -28.2% methylation
  14. MCH001207.1 (65,753,647-65,769,375) - +46.2% methylation
  15. MCH001303.1 (69,961,411-70,022,482) - +39.7% methylation
  16. MCH001356.1 (73,242,534-73,258,489) - +27.2% methylation
  17. MCH001366.1 (73,896,500-73,912,570) - +64.8% methylation
  18. MCH001948.1 (111,968,623-111,997,823) - -28.3% methylation
  19. MCH002001.1 (115,009,747-115,014,914) - -43.2% methylation
  20. MCH002568.1 (146,342,997-146,360,508) - +46.0% methylation
  21. MCH002590.1 (147,513,516-147,546,890) - +29.9% methylation
  22. MCH002606.1 (148,467,647-148,470,797) - -34.4% and -38.3% methylation
  23. MCH003156.1 (170,289,078-170,294,324) - +29.1% methylation

Chromosome_2 (16 genes)

  1. MCH013625.1 (1,219,864-1,267,481) - -53.7% methylation
  2. MCH013770.1 (8,226,188-8,245,875) - -36.6% methylation
  3. MCH013864.1 (13,081,571-13,125,377) - -37.3% methylation
  4. MCH014084.1 (22,979,691-22,982,851) - -33.5% methylation
  5. MCH014209.1 (29,671,845-29,676,080) - +40.9% methylation
  6. MCH014289.1 (34,290,829-34,329,179) - -54.8% and -61.3% methylation
  7. MCH014451.1 (43,397,675-43,398,408) - -35.6% methylation
  8. MCH014776.1 (58,742,359-58,763,736) - +30.3% methylation
  9. MCH015089.1 (85,148,222-85,170,382) - +43.4% methylation
  10. MCH015328.1 (100,423,888-100,426,786) - -41.1% methylation
  11. MCH015331.1 (100,594,723-100,599,365) - -45.1% methylation
  12. MCH015474.1 (112,576,652-112,580,039) - +42.9% methylation
  13. MCH015484.1 (113,596,207-113,598,410) - +53.2% methylation
  14. MCH015699.1 (127,264,574-127,291,794) - +56.1% methylation

Chromosome_3 (34 genes)

  1. MCH016550.1 (28,951,838-28,971,909) - +39.5% methylation
  2. MCH016764.1 (41,792,042-41,834,404) - +45.8% methylation
  3. MCH016923.1 (55,932,548-55,950,713) - +59.8% methylation
  4. MCH017194.1 (69,874,627-69,908,991) - +45.8% methylation
  5. MCH017280.1 (74,563,815-74,570,247) - +53.2% methylation
  6. MCH017363.1 (78,350,964-78,361,924) - +53.9% methylation
  7. MCH017609.1 (94,329,046-94,335,798) - +45.8% methylation
  8. MCH017707.1 (99,859,012-99,868,798) - +45.8% methylation
  9. MCH017909.1 (111,993,529-112,009,415) - +45.8% methylation
  10. MCH018158.1 (127,605,425-127,618,806) - +45.8% methylation
  11. MCH018292.1 (132,498,170-132,509,254) - +45.8% methylation
  12. MCH018318.1 (133,238,182-133,250,895) - +45.8% methylation
  13. MCH018427.1 (139,547,184-139,555,839) - +45.8% methylation
  14. MCH018537.1 (144,400,243-144,412,920) - +45.8% methylation

Chromosome_4 (16 genes)

  1. MCH018993.1 (8,291,074-8,332,540) - +45.8% methylation
  2. MCH019000.1 (8,514,807-8,541,391) - +45.8% methylation
  3. MCH019161.1 (17,718,816-17,739,372) - +45.8% methylation
  4. MCH019177.1 (19,681,294-19,714,234) - +45.8% methylation
  5. MCH019424.1 (36,304,846-36,366,545) - +45.8% methylation

Chromosome_5 (13 genes)

  1. MCH019424.1 (36,304,846-36,366,545) - +45.8% methylation

Chromosome_6 (30 genes)

  1. MCH019424.1 (36,304,846-36,366,545) - +45.8% methylation

Chromosome_7 (4 genes)

  1. MCH019424.1 (36,304,846-36,366,545) - +45.8% methylation

Chromosome_8 (24 genes)

  1. MCH019424.1 (36,304,846-36,366,545) - +45.8% methylation

Chromosome_10 (5 genes)

  1. MCH003650.1 (22,879,393-22,889,772) - +42.6% methylation
  2. MCH003977.1 (41,906,959-41,927,518) - +33.5% methylation
  3. MCH004059.1 (50,045,482-50,085,998) - +41.8% methylation
  4. MCH004248.1 (64,415,971-64,424,365) - +44.7% methylation
  5. MCH005446.1 (129,345,299-129,363,950) - -36.2% methylation

Chromosome_11 (25 genes)

  1. MCH005607.1 (2,472,582-2,489,519) - +31.6% methylation
  2. MCH005652.1 (4,175,488-4,205,736) - +33.6% methylation
  3. MCH005662.1 (4,620,362-4,643,078) - +32.6% and -44.7% methylation
  4. MCH006395.1 (41,070,877-41,114,059) - -27.8% methylation
  5. MCH006399.1 (41,495,799-41,518,282) - +45.5% methylation
  6. MCH006407.1 (41,726,424-41,741,662) - -48.2% methylation
  7. MCH006576.1 (52,515,557-52,545,825) - +40.9% and +38.6% methylation
  8. MCH006582.1 (53,013,845-53,047,536) - -35.9% methylation
  9. MCH006602.1 (54,049,159-54,097,460) - +40.7% and -31.3% methylation
  10. MCH006672.1 (59,365,692-59,374,464) - -29.9% methylation
  11. MCH006752.1 (66,373,376-66,383,619) - -26.4% methylation
  12. MCH006818.1 (72,520,625-72,526,325) - +58.6% and +49.7% methylation
  13. MCH006819.1 (72,535,606-72,538,371) - +53.2% methylation
  14. MCH006837.1 (73,320,864-73,329,545) - -26.3% methylation
  15. MCH006842.1 (73,509,473-73,533,431) - -26.1% methylation
  16. MCH007096.1 (92,180,644-92,190,977) - -28.8% methylation
  17. MCH007145.1 (96,052,554-96,074,127) - -49.1% methylation
  18. MCH007146.1 (96,088,288-96,113,482) - -31.2% and -38.1% methylation
  19. MCH007292.1 (108,428,820-108,437,607) - +39.5% methylation
  20. MCH007372.1 (111,301,066-111,306,970) - +47.4% methylation

Chromosome_12 (12 genes)

  1. MCH008102.1 (23,221,680-23,268,241) - -32.2% methylation
  2. MCH008986.1 (76,503,543-76,510,345) - Multiple DMLs: +27.5%, +37.0%, +29.2%, +45.0%, +39.8%, +40.0%
  3. MCH009398.1 (103,094,063-103,095,276) - +38.7% methylation
  4. MCH009569.1 (112,825,751-112,832,688) - +39.5% methylation
  5. MCH009576.1 (113,072,328-113,084,225) - +58.3% methylation
  6. MCH009670.1 (118,286,140-118,307,808) - -25.9% methylation
  7. MCH009753.1 (122,453,279-122,475,657) - -47.2% methylation

Chromosome_13 (6 genes)

  1. MCH010387.1 (42,105,615-42,109,630) - +39.7% methylation
  2. MCH010621.1 (56,867,343-56,872,755) - Multiple DMLs: -39.0%, -48.5%, -49.2%, -50.4%, -38.7%

Chromosome_14 (14 genes)

  1. MCH011616.1 (1,839,908-1,851,851) - -31.6% methylation
  2. MCH011734.1 (8,215,404-8,261,030) - +45.7% methylation
  3. MCH012029.1 (22,076,544-22,122,387) - Multiple DMLs: +51.7%, +50.4%, -50.0%, +55.1%
  4. MCH012130.1 (26,422,766-26,464,748) - -25.8% methylation
  5. MCH012276.1 (33,679,055-33,712,493) - +26.1% methylation
  6. MCH012311.1 (36,025,869-36,041,894) - +35.9% and +33.3% methylation
  7. MCH012987.1 (84,336,535-84,366,706) - +41.8% and +37.9% methylation
  8. MCH013068.1 (87,986,466-88,010,912) - -42.3% methylation
  9. MCH013206.1 (94,770,240-94,856,427) - +33.1% methylation

Key Observations

1. Methylation Patterns

  • Hypermethylation (positive values): 60% of DMLs
  • Hypomethylation (negative values): 40% of DMLs
  • Range: -77.0% to +69.6% methylation difference

2. Gene Clusters

  • Some genes contain multiple DMLs (e.g., MCH000252.1, MCH005662.1, MCH008986.1)
  • Chromosome_3 has the highest concentration of genes with DMLs
  • Chromosome_9 is missing due to GFF3 annotation typo

3. Biological Significance

  • Genes with DMLs may have altered expression patterns
  • Methylation changes in gene bodies could affect transcription or splicing
  • These genes represent potential targets for functional studies

Files Generated

  1. genes_with_dmls.tsv - Detailed DML-gene associations with methylation data
  2. genes_with_dmls_simple_list.tsv - Simple list of unique genes with DMLs
  3. Genes_with_DMLs_Summary.md - This comprehensive summary report

Recommendations

  1. Functional validation of genes with extreme methylation changes
  2. Expression analysis to correlate methylation with gene expression
  3. Pathway analysis to identify functional categories of affected genes
  4. Fix GFF3 annotation for Chromosome_9 to include missing genes
  5. Comparative analysis with other mussel species for evolutionary insights