Ying Lİ, Fang WANG, Xiaolong GAO, Lilin ZHU, Wen WANG, Kirill SHARSHOV

Comparative Analysis of the Heart Tissue Transcriptomes Between Low-altitude Reared and High-altitude Reared Bar-headed Geese (Anser indicus)

The bar-headed geese (Anser indicus) are renowned for high-altitude migratory fl ights and they must fl y over the Qinghai-Tibetan Plateaufor their annual migration. Through comparing the high-altitude bar-headed geese with the other closely related low-altitude species, manyeff orts have been made to reveal the unique adaptations at physiological, biochemical, and behavioral levels that help bar-headed geeseliving and fl ying in high-altitude conditions. Nonetheless, little is known about the transcriptome level changes of the bar-headed geeseadaptation to low-altitude environment. To explore the variations of gene expression that were induced by low-altitude environment inthe bar-headed geese, we conducted the first comparative transcriptomic analysis of heart tissues between bar-headed geese reared inhigh-altitude regions (~3000 m), and the bar-headed geese reared at the low-altitude regions (~30 m) for nearly three years. A total of 76diff erentially expressed genes (DEGs) were detected in the low-altitude bar-headed geese compared with the high-altitude bar-headedgeese. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly involvedin the focal adhesion, extracellular matrix (ECM) - receptor interaction, the mammalian target of rapamycin (mTOR) signaling pathway,wingless-type (Wnt) signaling pathway, and glycosaminoglycan degradation etc. The results will be useful for understanding the divergentadaptation of the bar-headed geese to diff erent altitude environment, and the transcriptome data provides a valuable resource for futurefunctional studies.

Düşük ve Yüksek İrtifalı Alanlarda Yetiştirilen Çubuk Başlı Kazlarda (Anser indicus) Kalp Dokusu Transkriptomlarının Karşılaştırmalı Analizi

Çubuk başlı kazlar (Anser indicus), yüksek irtifada göçmen uçuşlarıyla ünlüdür ve yıllık göçleri için Tibet Platosu üzerinden uçmaları gerekir. Yüksek irtifaya adapte çubuk başlı kazları, diğer yakından ilişkili alçak irtifalı türlerle karşılaştırarak, bu kazların yüksek irtifa koşullarında yaşamasına ve uçmasına yardımcı olan fizyolojik, biyokimyasal ve davranışsal seviyelerde benzersiz adaptasyonlarını ortaya çıkaracak birçok çalışma yapılmıştır. Bununla birlikte, çubuk başlı kazların alçak irtifalı ortamlara adaptasyonlarının transkriptom seviyesi değişiklikleri ile ilgili çok az şey bilinmektedir. Çubuk başlı kazlarda düşük irtifa ortamı tarafından indüklenen gen ekspresyon varyasyonlarını araştırmak için, yüksek irtifa bölgelerinde (~3000 m) yetiştirilen çubuk başlı kazlar arasındaki kalp dokularının ilk karşılaştırmalı transkriptomik analizini gerçekleştirdik ve bu kazlar yaklaşık üç yıl boyunca alçak irtifalı bölgelerde (~30 m) yetiştirildi. Yüksek irtifalı çubuk başlı kazlarla karşılaştırıldığında, alçak irtifalı çubuk başlı kazlarda farklı eksprese edilmiş (DEG) toplam 76 gen tespit edildi. Gen ontolojisi (GO) ve Kyoto Genler ve Genom Ansiklopedisi (KEGG) analizi, bu DEG’lerin temel olarak fokal adezyon, ekstrasellüler matris (ECM) - reseptör etkileşimi, rapamisin protein kompleksinin memeli hedefi (mTOR) sinyal yolu, wingless-tip (Wnt) sinyal yolu ve glikozaminoglikan degredasyonu vb. ile ilişkili oduğunu göstermiştir. Çalışma sonuçları, çubuk başlı kazların farklı irtifa ortamlarına farklı adaptasyonlarını anlamak için faydalı olacaktır ve elde edilen transkriptom verileri gelecekteki fonksiyonel çalışmalar için değerli bir kaynak imkanı sunacaktır.

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1. Takekawa JY, Heath SR, Douglas DC, Perry WM, Javed S, Newman SH, Suwal RN, Rahmani AR, Choudhury BC, Prosser DJ, Yan BP, Hou YS, Batbayar N, Natsagdorj T, Bishop CM, Butler PJ, Frappell PB, Milsom WK, Scott GR, Hawkes LA, Wikelski M: Geographic variation in bar-headed geese Anser indicus: Connectivity of wintering areas and breeding grounds across a broad front. Wildfowl, 59, 100-123, 2009.

2. Zhang Y, Hao M, Takekawa JY, Lei F, Yan B, Prosser DJ, Douglas DC, Xing Z, Newman SH: Tracking the autumn migration of the bar-headed goose (Anser indicus) with satellite telemetry and relationship to environmental conditions. Int J Zool, 2011:323847, 2011. DOI: 10.1155/2011/323847

3. Prins HHT, Wieren SE: Number, population structure and habitat use of bar-headed geese Anser indicus in Ladakh (India)during the brood-rearing period. Acta Zoologica Sinica, 50, 738-744, 2004.

4. Liu D, Zhang G, Li F, Ma T, Lu J, Qian F: A revised species population estimate for the bar-headed goose (Anser indicus) Avian Res, 8:7, 2017. DOI: 10.1186/s40657-017-0064-7

5. Hawkes LA, Balachandran S, Batbayar N, Butler PJ, Frappell PB, Milsom WK, Tseveenmyadag N, Newman SH, Scott GR, Sathiyaselvam P, Takekawa JY, Wikelski M, Bishop CM: The trans-Himalayan flights of barheaded geese (Anser indicus). Proc Natl Acad Sci USA, 108 (23): 9516-9519, 2011. DOI: 10.1073/pnas.1017295108

6. Hawkes LA, Balachandran S, Batbayar N, Butler PJ, Chua B, Douglas DC, Frappell PB, Hou Y, Milsom WK, Newman SH, Prosser DJ, Sathiyaselvam P, Scott GR, Takekawa JY, Natsagdorj T, Wikelski M, Witt MJ, Yan B, Bishop CM: The paradox of extreme high-altitude migration in bar-headed geese Anser indicus. Proc R Soc B, 280 (1750): 20122114, 2013. DOI: 10.1098/rspb.2012.2114

7. Swan LW: Goose of the Himalayas. Nat Hist, 79, 68-75, 1970.

8. Ward S, Bishop CM, Woakes AJ, Butler PJ: Heart rate and the rate of oxygen consumption of flying and walking barnacle geese (Branta leucopsis) and bar-headed geese (Anser indicus) J Exp Biol, 205 (21): 3347-3356, 2002.

9. Butler PJ: High fliers: The physiology of bar-headed geese. Comp Biochem Physiol A Mol Integr Physiol, 156 (3): 325-329, 2010. DOI: 10.1016/j. cbpa.2010.01.016

10. Scott GR, Hawkes LA, Frappell PB, Butler PJ, Bishop CM, Milsom WK: How bar-headed geese fly over the Himalayas. Physiology, 30 (2): 107-115, 2015. DOI: 10.1152/physiol.00050.2014

11. Scott GR, Milsom WK: Control of breathing and adaptation to high altitude in the bar-headed goose. Am J Physiol Regul Integr Comp Physiol, 93 (1): R379-R391, 2007. DOI: 10.1152/ajpregu.00161.2007

12. Scott GR: Elevated performance: The unique physiology of birds that fly at high altitudes. J Exp Biol, 214 (15): 2455-2462, 2011. DOI: 10.1242/ jeb.052548

13. Black CP, Tenney SM: Oxygen transport during progressive hypoxia in high-altitude and sea-level waterfowl. Respir Physiol, 39 (2): 217-239, 1980. DOI: 10.1016/0034-5687(80)90046-8

14. McCracken KG, Barger CP, Sorenson MD: Phylogenetic and structural analysis of the HbA (alphaA/betaA) and HbD (alphaD/betaA) hemoglobin genes in two high-altitude waterfowl from the Himalayas and the Andes: bar-headed goose (Anser indicus) and Andean goose (Chloephaga melanoptera). Mol Phylogenet Evol, 56 (2): 649-658, 2010. DOI: 10.1016/j. ympev.2010.04.034

15. Scott GR, Egginton S, Richards JG, Milsom WK: Evolution of muscle phenotype for extreme high altitude flight in the bar-headed goose. Proc Biol Sci, 276 (1673): 3645-3653, 2009. DOI: 10.1098/rspb.2009.0947

16. Jendroszek A, Malte H, Overgaard CB, Beedholm K, Natarajan C, Weber RE, Storz JF, Fago A: Allosteric mechanisms underlying the adaptive increase in hemoglobin-oxygen affinity of the bar-headed goose. J Exp Biol, 221 (Pt 18): jeb185470, 2018. DOI: 10.1242/jeb.185470

17. Natarajan C, Jendroszek A, Kumar A, Weber RE, Tame JRH, Fago A, Storz JF: Molecular basis of hemoglobin adaptation in the high-flying barheaded goose. PLOS Genet, 14(4):e1007331, 2018. DOI: 10.1371/journal. pgen.1007331

18. Bishop CM, Spivey RJ, Hawkes LA, Batbayar N, Chua B, Frappell PB, Milsom WK, Natsagdorj T, Newman SH, Scott GR, Takekawa JY, Wikelski M, Butler PJ: The roller coaster flight strategy of bar-headed geese conserves energy during Himalayan migrations. Science, 347 (6219): 250- 254, 2015. DOI: 10.1126/science.1258732

19. Cheviron ZA, Brumfield RT: Genomic insights into adaptation to high-altitude environments. Heredity, 108 (4): 354-361, 2012. DOI: 10.1038/ hdy.2011.85

20. Zhang G: Bird sequencing project takes off. Nature, 522:34, 2015. DOI: 10.1038/522034d

21. Wang W, Wang F, Hao R, Wang A, Sharshov K, Druzyaka A, Lancuo Z, Shi Y, Feng S: First de novo whole genome sequencing and assembly of the bar-headed goose. PeerJ, 8:e8914, 2020. DOI: 10.7717/peerj.8914

22. Hao Y, Xiong Y, Cheng Y, Song G, Lei F: Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. Proc Natl Acad Sci USA, 116 (24): 11851-11856, 2019. DOI: 10.1073/pnas.1819657116

23. Kim D, Langmead B, Salzberg SL: HISAT: A fast spliced aligner with low memory requirements. Nat Methods, 12 (4): 357-360, 2015. DOI: 10.1038/ nmeth.3317

24. Liao Y, Smyth GK, Shi W: Feature counts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30 (7): 923-930, 2014. DOI: 10.1093/bioinformatics/btt656

25. Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15 (12): 550, 2014. DOI: 10.1186/s13059-014-0550-8

26. Yu G, Wang LG, Han Y, He QY: Clusterprofiler: An r package for comparing biological themes among gene clusters. OMICS, 16 (5): 284-287, 2012. DOI: 10.1089/omi.2011.0118

27. Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods, 25 (4): 402- 408, 2001. DOI: 10.1006/meth.2001.1262

28. Qi X, Zhang Q, He Y, Yang L, Zhang X, Shi P, Yang L, Liu Z, Zhang F, Liu F, Liu S, Wu T, Cui C, Ouzhuluobu, Bai C, Baimakangzhuo, Han J, Zhao S, Liang C, Su B: The transcriptomic landscape of yaks reveals molecular pathways for high altitude adaptation. Genome Biol Evol, 11 (1): 72-85, 2019. DOI: 10.1093/gbe/evy264

29. Dohn TE, Waxman JS: Distinct phases of Wnt/β-catenin signaling direct cardiomyocyte formation in zebrafish. Dev Biol, 361 (2): 364-376, 2012. DOI: 10.1016/j.ydbio.2011.10.032

30. Deb A: Cell-cell interaction in the heart via Wnt/β-catenin pathway after cardiac injury. Cardiovasc Res, 102 (2): 214-223, 2014. DOI: 10.1093/cvr/ cvu054

31. Williams C, Sullivan K, Black LD: Partially digested adult cardiac extracellular matrix promotes cardiomyocyte proliferation in vitro. Adv Healthc Mater, 4 (10): 1545-1554, 2015. DOI: 10.1002/adhm.201500035

32. Daquinag AC, Gao Z, Fussell C, Sun K, Kolonin MG: Glycosaminoglycan modification of decorin depends on MMP14 activity and regulates collagen assembly. Cells, 9(12):2646, 2020. DOI: 10.3390/cells9122646