Chain file request for comparative analysis of lactation gene evolution

[xmmmr]

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