Chain file request for comparative analysis of lactation gene evolution

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xmmmr

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Apr 15, 2026, 6:30:30 AMApr 15
to gen...@soe.ucsc.edu
Dear UCSC Genome Browser Team,
Thank you very much for the invaluable support your team provides to scientific research worldwide.
I am a researcher studying mammary gland evolution and lactation mechanisms across mammals. My current project focuses on comparative genomic analyses between goat (Capra hircus, assembly ARS1, GCA_001704415.2) and representative species spanning all three major mammalian clades: monotremes, marsupials, and eutherians.
To perform reliable cross-species coordinate conversion (liftOver) and whole-genome comparative analyses, I sincerely request your help in generating pairwise alignment chain files between goat ARS1 and the following reference assemblies:
A. Monotremata
  1. Platypus (Ornithorhynchus anatinus) – mOrnAna1.p.v1 (GCA_004115215.2)
  2. Short-beaked echidna (Tachyglossus aculeatus) – mTacAcu1.pri (GCF_015852505.1)
B. Marsupialia
  1. Gray short-tailed opossum (Monodelphis domestica) – ASM229v1 (GCA_000002295.1)
  2. Sugar glider (Petaurus breviceps) – PetGlider_PUasm1.0 (GCF_028583685.1)
  3. Tasmanian devil (Sarcophilus harrisii) – mSarHar1.11 (GCF_902635505.1)
  4. Koala (Phascolarctos cinereus) – phaCin_unsw_v4.1 (GCA_002099425.1)
  5. Tammar wallaby (Notamacropus eugenii) – Meug_1.0 (GCA_000004035.1)
C. Eutheria
  1. Rat (Rattus norvegicus) – GRCr8 (GCA_036323735.1)
  2. Human (Homo sapiens) – GRCh38.p14 (GCA_000001405.29)
  3. Cattle (Bos taurus) – ARS-UCD2.0 (GCA_002263795.4)
  4. Sheep (Ovis aries) – ARS-UI_Ramb_v3.0 (GCA_016772045.2)
  5. Horse (Equus caballus) – EquCab3.0 (GCA_002863925.1)
  6. Donkey (Equus asinus) – ASM1607732v2 (GCA_016077325.2)
  7. Arabian camel (Camelus dromedarius) – CamDro2 (GCA_000803125.2)
  8. Bactrian camel (Camelus bactrianus) – ASM4877302v1 (GCF_048773025.1)
  9. Rabbit (Oryctolagus cuniculus) – OryCun2.0 (GCA_000003625.1)
  10. Cat (Felis catus) – F.catus_Fca126_mat1.0 (GCA_018350175.1)
  11. Dog (Canis lupus familiaris) – ROS_Cfam_1.0 (GCA_014441545.1)
  12. Rhesus macaque (Macaca mulatta) – Mmul_10 (GCA_003339765.3)
  13. Water buffalo (Bubalus bubalis) – Bubbub1.0 (GCA_019923935.1)
  14. African elephant (Loxodonta africana) – Loxafr3.0 (GCA_000001905.1)
  15. Harbor seal (Phoca vitulina) – GSC_HSeal_1.0 (GCF_004348235.1)
  16. Guinea pig (Cavia porcellus) – Cavpor3.0 (GCA_000151735.1)
  17. Sika deer (Cervus nippon) – mCerNip1.1 (GCA_034195675.1)
  18. Chimpanzee (Pan troglodytes) – Pan_tro_3.0 (GCA_000001515.5)
  19. Large flying fox (Pteropus vampyrus) – pteVam1 (GCA_000002945.2)
  20. Blue whale (Balaenoptera musculus) – mBalMus1.v2 (GCA_009873245.2)
  21. Chinese hamster (Cricetulus griseus) – CriGri-PICRH-1.0 (GCA_003668045.2)
These chain files will greatly facilitate my research on the evolutionary dynamics of mammary-specific regulatory elements (enhancers) and lactation-related genes across mammals.
If any of these assemblies are not suitable for direct alignment, or if additional information is needed, please kindly let me know.
Thank you so much for your time and assistance. I greatly appreciate your work maintaining the UCSC Genome Browser and supporting the global research community.
Best regards,
Xiaoyu Mi
Key Laboratory of Animal Biotechnology, Ministry of Agriculture
Yangling 712100, Shaanxi, P.R.China
Email: mxy13...@163.com

Jairo Navarro Gonzalez

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Apr 24, 2026, 5:00:56 PMApr 24
to xmmmr, gen...@soe.ucsc.edu

Dear Xiaoyu Mi,

Thank you for your patience. We have generated pairwise liftOver chain
files between goat ARS1.2 (GCF_001704415.2) and 17 of the assemblies
you requested. They are now publicly available on our hgdownload
server, in both directions (goat -> species and species -> goat).

From goat ARS1.2 to other speciesFrom other species to goat ARS1.2Cattle and sheep (already public, included for completeness)Notes and substitutions
  • Tammar wallaby: the requested assembly GCA_000004035.1 (Meug_1.0) is
    not in our system. We used the newer assembly GCF_028372415.1
    (mMacEug1.pri_v2) instead.
  • Echidna (GCF_015852505.1) and human (hg38, GRCh38.p14) are still in
    progress; we will follow up once those are released.
  • The following requested species could not be aligned in this batch
    due to pipeline issues and are not yet available: platypus, gray
    short-tailed opossum, koala, horse, Arabian camel, rhesus macaque,
    and chimpanzee. We may revisit these in a future round.

Please let us know if you run into any trouble downloading or using
the chain files.

Best regards,
UCSC Genome Browser team


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xmmmr

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Apr 27, 2026, 3:00:30 AMApr 27
to Jairo Navarro Gonzalez, gen...@soe.ucsc.edu

Dear UCSC Genome Browser Team,
Thank you very much for your hard work and great support. I really appreciate that you have successfully generated the pairwise liftOver chain files between goat ARS1.2 and the 17 requested mammalian assemblies.
It is of great value for our ongoing comparative genomics and mammalian lactation evolution research. Thanks again for sharing these important data and making them publicly available.
I understand that several species, including platypus, opossum, koala, horse, camel, macaque and chimpanzee, were not completed in this round due to pipeline limitations, and that echidna and human are still ongoing.
These species are indispensable for our cross-species mammary gland and lactation evolution study. I would highly appreciate it if you could process them in a future pipeline run whenever possible.
Thank you again for your ongoing support. Please let me know if I can provide any further information.
Best regards,
Xiaoyu Mi



Clay Fischer

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Apr 30, 2026, 2:30:44 PMApr 30
to xmmmr, gen...@soe.ucsc.edu
Dear Xiaoyu Mi,

This process is underway and may take some days to complete. We will let you know when it is finished.

Thanks,
--
Clay


To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/168b6a6c.5d7b.19dcda33a7b.Coremail.mxy13130916%40163.com.

Gerardo Perez

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May 28, 2026, 12:36:30 AM (3 days ago) May 28
to xmmmr, gen...@soe.ucsc.edu

Hello, Xiaoyu Mi.

We have made the requested chain files available on our download server. Please note that for some chain files, we used an equivalent version of the assembly:

Echidna (GCF_015852505.1) to goat (GCF_001704415.2)

GCF_015852505.1 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/015/852/505/GCF_015852505.1/liftOver/GCF_015852505.1ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_015852505.1: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_015852505.1.over.chain.gz

Platypus (GCF_004115215.2) to goat (GCF_001704415.2)

GCF_004115215.2 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/004/115/215/GCF_004115215.2/liftOver/GCF_004115215.2ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_004115215.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_004115215.2.over.chain.gz

Opossum (GCF_000002295.2) to goat (GCF_001704415.2)

GCF_000002295.2 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/295/GCF_000002295.2/liftOver/GCF_000002295.2ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_000002295.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_000002295.2.over.chain.gz

Koala (GCF_002099425.1) to goat (GCF_001704415.2)

GCF_002099425.1 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/002/099/425/GCF_002099425.1/liftOver/GCF_002099425.1ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_002099425.1: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_002099425.1.over.chain.gz

Horse (GCF_002863925.1) to goat (GCF_001704415.2)

GCF_002863925.1 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/002/863/925/GCF_002863925.1/liftOver/GCF_002863925.1ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_002863925.1: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_002863925.1.over.chain.gz

Arabian camel (GCF_000803125.2) to goat (GCF_001704415.2)

GCF_000803125.2 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/000/803/125/GCF_000803125.2/liftOver/GCF_000803125.2ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_000803125.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_000803125.2.over.chain.gz

Rhesus macaque (GCF_003339765.1) to goat (GCF_001704415.2)

GCF_003339765.1 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/hubs/GCF/003/339/765/GCF_003339765.1/liftOver/GCF_003339765.1ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> GCF_003339765.1: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCF_003339765.1.over.chain.gz

Chimpanzee (GCF_000001515.7) to goat (GCF_001704415.2)

panTro5 (GCF_000001515.7) -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/liftOver/panTro5ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> panTro5 (GCF_000001515.7): https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToPanTro5.over.chain.gz

Human (hg38) to goat (GCF_001704415.2)

hg38 -> GCF_001704415.2: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCF_001704415.2.over.chain.gz

GCF_001704415.2 -> hg38: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToHg38.over.chain.gz

I hope this is helpful. If you have any questions or need further assistance, please feel free to reach out to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute


To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAEiWAORA7MLQvN5mG8FnQROAp5-T2HWQXWuMmQ1iaOBJJSP9tw%40mail.gmail.com.

xmmmr

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May 29, 2026, 5:00:37 AM (2 days ago) May 29
to Gerardo Perez, gen...@soe.ucsc.edu
Dear UCSC Genome Browser Team,
Thanks again for sharing these important data and making them publicly available.



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