Dr. Paolo Franchini
Biology
Building M, Room M825a
University of Konstanz
Universitätsstr. 10
78457 Konstanz
Tel: +49 (0) 7531 884405
E-mail: [email protected]
Building M, Room M825a
University of Konstanz
Universitätsstr. 10
78457 Konstanz
Tel: +49 (0) 7531 884405
E-mail: [email protected]
I am broadly interested in the fields of evolutionary biology and population genetics. I am currently exploring several lines of research to identify the genetic basis of adaptive traits in the Mesoamerican fishes of the Midas cichlid species complex (the Amphilophus citrinellus species group). I am particularly interested in the role of transcriptome differentiation and of the miRNA regulatory system in the evolutionary diversification of the cichlid fishes.
You can download my full CV here
You can download my full CV here
Publications
Google Scholar Profile
49. Meyer A†, Schloissnig S†, Franchini P†, Kang D†, Woltering J†, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink H, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M (In press) Giant Lungfish genome elucidates the conquest of land by vertebrates. Nature.
†These authors contributed equally to this work.
48. Rhie A, McCarthy SA, Fedrigo O, …, Franchini P (40/121), …, Jarvis ED (In press) Towards complete and error-free genome assemblies of all vertebrate species. Nature.
47. Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P* (In press) The Comparative Genomic Landscape of Adaptive Radiation in Crater Lake Cichlid Fishes. Molecular Ecology.
*Corresponding author
46. Kautt AF, Kratochwil CF, Nater A, Machado-Schiaffino G, Olave M, Henning F, Torres-Dowdall J, Härer A, Hulsey CD, Franchini P, Pippel M, Myers EW, Meyer A (2020) Contrasting signatures of genomic divergence during sympatric speciation. Nature 588, 106-111.
45. Fruciano C, Colangelo P, Castiglia R, Franchini P* (2020) Does divergence from normal patterns of integration increase as chromosomal fusions increase in number? A test on a house mouse hybrid zone. Current Zoology 66, 527-538.
*Corresponding author
44. Real FM, Haas SA, Franchini P et al. (2020) The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 370, 208-214.
43. Franchini P*, Kautt A, Nater A, Antonini G, Castiglia R, Meyer A, Solano E (2020) Reconstructing the evolutionary history of chromosomal races on islands: a genome wide analysis of natural house mouse populations. Molecular Biology and Evolution 37, 2825-2837.
*Corresponding author
42. Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D (2020). Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway. iScience 23, 101510.
41. Raffini F, Schneider FR, Franchini P, Kautt AF, Meyer A (2020) Diving into divergence: adaptive differentiation in swimming performances, physiology and gene expression between sympatric cichlid fishes. Molecular Ecology 29, 1219-1234.
Perspective on the article in the "News and Views" section of the journal (Gaither MR, Greaves S, Amirthalingam P. 2020. The physiology of rapid ecological specialization: A look at the Midas cichlids. Molecular Ecology 29, 1215-1218).
40. Franchini P*, Xiong P, Fruciano C, Schneider FR, Woltering J, Hulsey CD, Meyer A (2019) MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Molecular Biology and Evolution 36, 2498-2511.
*Corresponding author
39. Xiong P, Schneider FR, Hulsey CD, Meyer A, Franchini P* (2019) Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes. Scientific Reports 9, 13848.
*Corresponding author
38. Fruciano C, Meyer A, Franchini P* (2019) Divergent allometric trajectories in gene expression and coexpression produce species differences in sympatrically speciating Midas cichlid fish. Genome Biology and Evolution 11, 1644-1657.
*Corresponding author
37. Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M (2018) Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nature Communications 9, 5136.
36. Irisarri I, Singh P, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon A, Lemmon E, Thallinger G, Sturmbauer C, Meyer A (2018). Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nature Communications 9, 3159.
35. Xiong P, Hulsey CD, Meyer A, Franchini P* (2018). Evolutionary divergence of 3′ UTRs in cichlid fishes. BMC Genomics 19, 433.
*Corresponding author
34. Burrichter A, Denger K, Franchini P, Huhn T, Müller N, Spiteller D, Schleheck D (2018) Anaerobic degradation of the plant sugar sulfoquinovose concomitant with H2S production: Escherichia coli K-12 and Desulfovibrio sp. strain DF1 as co-culture model. Frontiers in Microbiology 9, 2792.
33. Lee HJ, Manousaki T, Kang JY, Lein E, Franchini P, Meyer A (2017) Genome-Wide Transcriptional Left-Right Asymmetry in the Brain in Lateralized Scale-Eating Cichlid Fish, Perissodus microlepis. Genome Biology and Evolution 9, 3122-3136.
32. Franchini P, Irisarri I, Fudickar A, Schmidt A, Meyer A, Wikelski M, Partecke J (2017) Animal tracking meets migration genomics: transcriptomic analysis of a partially migratory bird species. Molecular Ecology 26, 3204-3216.
31. Franchini P, Monne-Parera D, Kautt A, Meyer A (2017) quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a non-radiating cichlid lineage. Molecular Ecology 26, 2783-2795.
30. Raffini F, Fruciano C, Franchini P, Meyer A (2017) Towards understanding the genetic basis of mouth asymmetry in the scale‐eating cichlid Perissodus microlepis. Molecular Ecology 26, 77-91.
29. Franchini P, Xiong P, Fruciano C, Meyer A (2016) The role of microRNAs in the repeated parallel diversification of lineages of Midas cichlid fish from Nicaragua. Genome Biology and Evolution 8, 1543-1555.
28. Franchini P*, Colangelo P, Meyer A, Fruciano C (2016) Chromosomal rearrangements, phenotypic variation and modularity: a case study from a contact zone between house mouse Robertsonian races in Central Italy. Ecology and Evolution 6, 1353-1362.
*Corresponding author
27. Fruciano C†, Franchini P†, Kovacova V, Elmer K, Henning F, Meyer A (2016) Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nature Communications 7, 12736.
†These authors contributed equally to this study
26. Fruciano C, Franchini P, Raffini F, Fan S, Meyer A (2016) Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecology and Evolution 6, 4102–4114.
25. Felux A-K, Franchini P, Schleheck D (2015) Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. Standards in Genomic Sciences 10, 1.
24. Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A (2015) Transcriptomics of two evolutionary novelties: how to make a sperm‐transfer organ out of an anal fin and a sexually selected “sword” out of a caudal fin. Ecology and Evolution 5, 848-864.
23. Kavembe GD, Franchini P, Irisarri I, Machado-Schiaffino G, Meyer A (2015) Genomics of adaptation to multiple concurrent stresses: insights from comparative transcriptomics of a Cichlid fish from one of earth’s most extreme environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa. Journal of Molecular Evolution 81, 90-109.
22. Modica MV, Lombardo F, Franchini P, Oliverio M (2015) The venomous cocktail of the vampire snail Colubraria reticulata (Mollusca, Gastropoda). BMC genomics 16, 1.
21. Franchini P†, Fruciano C†, Frickey T, Jones JC, Meyer A (2014) The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs. PLoS One 9, e95027.
†These authors contributed equally to this work.
20. Franchini P†, Fruciano C†, Spreitzer ML, Jones JC, Elmer KR, Henning F, Meyer A (2014) Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes. Molecular Ecology 23, 1828-1845.
†These authors contributed equally to this work.
Perspective on the article in the "News and Views" section of the journal (Rogers SM, Jamniczky HA. 2014. The shape of things to come in the study of the origin of species? Molecular Ecology 23, 1650-1652.)
19. Elmer KR, Fan S, Kusche H, Spreitzer ML, Kautt A, Franchini P, Meyer A (2014) Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes. Nature Communications 5, 5168.
18. Seehausen Ole, Butlin RK, Keller I, …, Franchini P (17/33), …, Wiedmer A (2014) Genomics and the origin of species. Nature Reviews Genetics 15, 176-192.
17. Henning F, Lee HJ, Franchini P, Meyer A (2014) Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Molecular ecology 23, 5224-5240.
Perspective on the article in the "News and Views" section of the journal (Hohenlohe PA. 2014. Ecological genomics in full colour. Molecular Ecology 23: 5129-5131.)
16. Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A (2013) Shaping development through mechanical strain: the transcriptional basis of diet‐induced phenotypic plasticity in a cichlid fish. Molecular Ecology 22, 4516-4531.
Perspective on the article in the "News and Views" section of the journal (Young RL 2013. Linking conceptual mechanisms and transcriptomic evidence of plasticity-driven diversification. Molecular Ecology 22: 4363-4365.)
15. Henning F, Jones JC, Franchini P, Meyer A (2013) Transcriptomics of morphological color change in polychromatic Midas cichlids. BMC Genomics 14, 1.
14. Jones JC, Fan S, Franchini P, Schartl M, Meyer A (2013) The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome‐wide approach using restriction site‐associated DNA sequencing. Molecular Ecology 22, 2986-3001.
13. Fruciano C, Franchini P, Meyer A (2013) Resampling-based approaches to study variation in morphological modularity. PLoS One 8, e69376.
12. Manousaki T, Hull PM, Kusche H, Machado-Schiaffino G, Franchini P, Harrod C, Elmer KR, Meyer A (2013) Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick‐lipped Midas cichlid fishes from Nicaragua. Molecular Ecology 22, 650-669.
11. Solano E, Franchini P, Colangelo P, Capanna E, Castiglia R (2013) Multiple origins of the western European house mouse in the Aeolian Archipelago: clues from mtDNA and chromosomes. Biological Invasions 15, 729-739.
10. Franchini P*, Sola L, Crosetti D, Milana V, Rossi AR (2012) Low levels of population genetic structure in the gilthead sea bream, Sparus aurata, along the coast of Italy. ICES Journal of Marine Science: Journal du Conseil 69, 41-50.
*Corresponding author
9. Milana V, Franchini P, Sola L, Angiulli E, Rossi AR (2012) Genetic structure in lagoons: the effects of habitat discontinuity and low dispersal ability on populations of Atherina boyeri. Marine Biology 159, 399-411.
8. Colangelo P, Aloise G, Franchini P, Annesi F, Amori G (2012) Mitochondrial DNA reveals hidden diversity and an ancestral lineage of the bank vole in the Italian peninsula. Journal of Zoology 287, 41-52.
7. Franchini P, Van der Merwe M, Roodt-Wilding R (2011) Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis. BMC Research Notes 4, 1.
6. Rossi AR, Miggiano M, Crosetti D, Franchini P, Sola L (2009) Genetic comparison of temporal replicates of gilthead sea bream (Sparus aurata) from two Tyrrhenian coastal lagoons characterized by different management. Journal of Applied Ichthyology 25, 603-605.
5. Van der Merwe M, Franchini P, Roodt-Wilding R (2011) Differential growth-related gene expression in abalone (Haliotis midae). Marine Biotechnology 13, 1125-1139.
4. Franchini P*, Colangelo P, Solano E, Capanna E, Verheyen E, Castiglia R (2010) Reduced gene flow at pericentromeric loci in a hybrid zone involving chromosomal races of the house mouse Mus musculus domesticus. Evolution 64, 2020-2032.
*Corresponding author
3. Franchini P, Slabbert R, Merwe MVD, Roux A, Roodt-Wilding R (2010) Karyotype and genome size estimation of Haliotis midae: estimators to assist future studies on the evolutionary history of Haliotidae. Journal of Shellfish Research 29, 945-950.
2. Colangelo P, Castiglia R, Franchini P, Solano E (2010) Pattern of shape variation in the eastern African gerbils of the genus Gerbilliscus (Rodentia, Muridae): Environmental correlations and implication for taxonomy and systematics. Mammalian Biology-Zeitschrift für Säugetierkunde 75, 302-310.
1. Franchini P*, Castiglia R, Capanna E (2008) Reproductive isolation between chromosomal races of the house mouse Mus musculus domesticus in a parapatric contact area revealed by an analysis of multiple unlinked loci. Journal of Evolutionary Biology 21, 502-513.
*Corresponding author