MoZoo Lab – Mitogenomics and Evolution

Scientific publications by Marco Passamonti

  1. Marturano G., Carli D., Cucini C., Carapelli A., Plazzi F., Frati F., Passamonti M.*, Nardi F. (2024). SmithHunter: a novel, unified workflow for the identification of candidate smithRNAs and their targets. BMC Bioinformatics, 25:286. (*corresponding author).
  2. Muneretto G., Plazzi F., Passamonti M. (2024). Mitochondrion-to-nucleus communication mediated by RNA export: a survey of potential mechanisms and players across eukaryotes. BIOLOGY LETTERS, 20:20240147.
  3. Formaggioni A., Cavalli G., Hamada M., Sakamoto T., Plazzi F., Passamonti M. (2024). The evolution and characterization of RNA interference pathways in Lophotrochozoa. GENOME BIOLOGY AND EVOLUTION,16(5): evae098.
  4. Plazzi F., Le Cras Y., Formaggioni A., Passamonti M. (2023). Mitochondrally-mediated RNA interference, a retrograde signaling system affecting nuclear gene expression. HEREDITY, 132(3): 156-161.
  5. Santovito D., Brustenga L., Lucentini L., Plazzi F., Chiesa S., Passamonti M. (2023) Mitochondrial genomics of understudied marine phyla: negative evidence for sex-linked heteroplasmy in the nemertean worm Notospermus geniculatus (Delle Chiaje, 1822). SUSTAINABILITY, 15: 10212.
  6. Xu R., Martelossi J., Smits M., Iannello M., Peruzza L., Babbucci M., Milan M., Dunham J.P., Breton S., Milani L., Nuzhdin S.V., Bargelloni L., Passamonti M., Ghiselli F. (2022). Multi-tissue RNA-Seq analysis reveal complex gene regulation and molecular evolution in the Manila clam. GENOME BIOLOGY AND EVOLUTION, 14(12) evac171.
  7. Formaggioni A., Plazzi F., Passamonti M. (2022). Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. SCIENTIFIC REPORTS, 11040.
  8. Plazzi F., Puccio G., Passamonti M. (2021). HERMES: An Improved Method to Test Mitochondrial Genome Molecular Synapomorphies among Clades. MITOCHONDRION, 58:285-295.
  9. Passamonti M., Calderone M., Delpero M., Plazzi F. (2020). Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs. SCIENTIFIC REPORTS, 10: 8219.
  10. Passamonti M., Plazzi F. (2020). DUI and beyond: the contribution of the Manila clam Ruditapes philippinarum. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 58:529-540.
  11. Ghiselli F., Maurizii M.G., Reunov A., Ariño H., Cifaldi C., Pecci A., Alexandrova Y., Bettini S., Passamonti M., Franceschini V., Liliana Milani L. (2019). Natural heteroplasmy and mitochondrial inheritance in Bivalve Molluscs. INTEGRATIVE AND COMPARATIVE BIOLOGY, 59(4): 1016-1032.
  12. Iannello M., Puccio G., Piccinini G., Passamonti M., Ghiselli F. (2019) The dynamics of mito-nuclear coevolution: a perspective from bivalve species with two different mechanisms of mitochondrial inheritance. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 57: 534-547.
  13. Plazzi F., Passamonti M. (2019) Footprints of unconventional mitochondrial inheritance in bivalve phylogeny: signatures of positive selection on clades with Doubly Uniparental Inheritance. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 57(2) 258-271.
  14. Renaut S., Guerra D., Hoeh w.R., Stewart D.T., Bogan A.E., Ghiselli F., Milani L., Passamonti M., Breton S. (2018). Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using hybrid de novo assembly approach. GENOME BIOLOGY AND EVOLUTION, 10(7): 1637-1646.
  15. Ghiselli F., Iannello M., Puccio G., Chang P., Plazzi F., Nuzhdin S., Passamonti M. (2018) Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes. GENOME BIOLOGY AND EVOLUTION, 10(6): 1389-1402.
  16. Punzi E., Milani L., Ghiselli F., Passamonti M. (2018). Lose it or keep it: (how bivalves can provide) insights into mitochondrial inheritance mechanisms. JOURNAL OF EXPERIMENTAL ZOOLOGY, PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION, 330: 41-51.
  17. Milani, L., Pecci A., Ghiselli F., Passamonti M., Lazzari M., Franceschini V., Maurizii M.G. (2017). Germ cell line during the seasonal sexual rest of clams: finding niches of cells for gonad renewal. HISTOCHEMISTRY AND CELL BIOLOGY, 149:105-110.
  18. Ghiselli F., Milani L., Iannello M., Procopio E., Chang P.L., Nuzhdin S.V., Passamonti M. (2017). The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PEERJ, 5:e3692.
  19. Pozzi A., Plazzi F., Milani L., Ghiselli F., Passamonti M. (2017). SmithRNAs: could mitochondria “bend” nuclear regulation? MOLECULAR BIOLOGY AND EVOLUTION, 34(8): 1960-1973.
  20. Milani L., Pecci A., Ghiselli F., Passamonti M., Franceschini V., Maurizii M. (2017). Vasa expression suggests shared germ line dynamics in bivalve molluscs. HISTOCHEMISTRY AND CELL BIOLOGY, 148:157-171.
  21. Plazzi F., Puccio G., Passamonti M. (2017). Burrowers from the past: mitochondrial signatures of Ordovician bivalve infaunalization. GENOME BIOLOGY AND EVOLUTION, 9(4):956-967.
  22. Milani L., Ghiselli F., Passamonti M. (2016). Mitochondrial selfish elements and the evolution of biological novelties. CURRENT ZOOLOGY, 62(6):687-697.
  23. Gusman A., Lecomte S., Stewart D. T., Passamonti M., Breton S., (2016). Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA. PEER J, 4:e2760.
  24. Plazzi F., Puccio G., Passamonti M. (2016). Comparative large-scale mitogenomics evidences clade-specific evolutionary trends in mitochondrial DNAs of Bivalvia. GENOME BIOLOGY AND EVOLUTION, 8(8): 2544-2564.
  25. Capt C., Passamonti M., Breton S. (2016). The human mitochondrial genome may code for more than 13 proteins. MITOCHONDRIAL DNA, 27(5): 3098-3101.
  26. Bettinazzi S., Plazzi F., Passamonti M. (2016). The complete female- and male-transmitted mitochondrial genome of Meretrix lamarckii: a new step towards the characterization of Doubly Uniparental Inheritance in venerid bivalves. PLoS ONE, 11(4): e0153631.
  27. Nishihara H., Plazzi F., Passamonti M., N Okada N. (2016). MetaSINEs: broad distribution of a novel SINE superfamily in animals. GENOME BIOLOGY AND EVOLUTION, 8(3): 528-539.
  28. Guerra D., Ghiselli F., Milani L., Breton S., Passamonti M. (2016). Early replication dynamics of sex-linked mitochondrial DNAs in the doubly uniparental inheritance species Ruditapes philippinarum (Bivalvia Veneridae). HEREDITY, 116: 324-332.
  29. Milani L., Ghiselli F., Pecci A., Maurizii M.G., Passamonti M. (2015). The expression of a novel mitochondrially-encoded gene in gonadic precursors may drive paternal inheritance of mitochondria. PLoS ONE, 10(9): e0137468.
  30. Milani L., Maurizii M.G., Pecci A., Ghiselli F., Passamonti M. (2015). Localization and dynamics in the bivalve species Ruditapes philippinarum. MOLECULAR REPRODUCTION AND DEVELOPMENT, 82: 406-407.
  31. Milani L., Scali V., Passamonti M. (2015). Speciation through androgenesis in the stick insect genus Clonopsis (Insecta Phasmatodea). JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 53(2): 116-123.
  32. Plazzi F., Cassano A., Passamonti M. (2015). The quest for Doubly Uniparental Inheritance in heterodont bivalves and its invention in Meretrix lamarckii (Veneridae: Meretricinae). JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 53(1): 87-94 .
  33. Breton S., Milani L., Ghiselli F., Guerra D., Stewart D.T., Passamonti M. (2014). A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs. TRENDS IN GENETICS, 30(12): 555-564.
  34. Milani L., Ghiselli F., Iannello M., Passamonti M. (2014). Evidence for somatic transcription of male-transmitted mitochondrial genome in the DUI species Ruditapes philippinarum (Bivalvia: Veneridae). CURRENT GENETICS, 60: 163-173.
  35. Milani L., Ghiselli F., Maurizii M.G., Nuzhdin S., Passamonti M. (2014). Paternally transmitted mitochondria express a new gene of potential viral origin. GENOME BIOLOGY AND EVOLUTION, 6(2):391–405.
  36. Guerra D., Ghiselli F., Passamonti, M. (2014). The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae). GENE, 536(2): 316-325.
  37. Ghiselli F., Milani L., Guerra D., Chang P.L., Breton S., Nuzhdin S.V., Passamonti M. (2013). Structure, transcription and variability of metazoan mitochondrial genome. Perspectives from an unusual mitochondrial inheritance system. GENOME BIOLOGY AND EVOLUTION 5(8): 1535-1554.
  38. Milani L., Ghiselli F., Guerra D., Breton S., Passamonti M. (2013). A comparative analysis of Mitochondrial ORFans: new clues on their origin and role in species with Doubly Uniparental Inheritance. GENOME BIOLOGY AND EVOLUTION 5(7): 1408-1434.
  39. Milani L., Ghiselli F., Nuzhdin S., Passamonti M. (2013). Nuclear genes with sex bias in Ruditapes philippinarum (Bivalvia, Veneridae): mitochondrial inheritance and sex determination in DUI species. JOURNAL OF EXPERIMENTAL ZOOLOGY, PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION, 320B: 442-454.
  40. Plazzi F., Ribani A., Passamonti M. (2013). The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera. BMC GENOMICS, 14:409.
  41. Scali V., Milani L., Passamonti M. (2013). Description and ecology of new Pijnackeria stick insects: four bisexual species and a triploid parthenogen, with their phyletic relationships. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, 51(3): 213-226.
  42. Milani L., Ghiselli F., and Passamonti M. (2012). Sex-linked mitochondrial behavior during early embryo development in Ruditapes philippinarum (Bivalvia Veneridae) a species with the Doubly Uniparental Inheritance (DUI) of mitochondria. JOURNAL OF EXPERIMENTAL ZOOLOGY, PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION, 318(3): 182-189.
  43. Scali V., Milani L., Passamonti M. (2012). Revision of the stick insect genus Leptynia: description of new taxa, speciation mechanism and phylogeography. CONTRIBUTIONS TO ZOOLOGY, 81(1): 25-42.
  44. Ghiselli F., Milani L., Chang P.L., Hedgecock D., Davis J.P., Nuzhdin S.V., Passamonti M. (2012) De novo assembly of Ruditapes philippinarum transcriptome provides new insights on expression bias, mitochondrial Doubly Uniparental Inheritance and sex determination. MOLECULAR BIOLOGY AND EVOLUTION, 29(2): 771-786.
  45. Milani L., Ghiselli F., Maurizii M.G., Passamonti M. (2011). Doubly Uniparental Inheritance of Mitochondria as a model system for studying germ line formation. PLOS ONE, 6(11): e28194.
  46. Plazzi F., Ceregato A., Taviani M., Passamonti M. (2011). A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes. PLOS ONE, 6(11): e27174.
  47. Passamonti M., Ricci A., Milani L., Ghiselli F. (2011) Mitochondrial genomes and Doubly Uniparental Inheritance: new insights from Musculista senhousia sex-linked mitochondrial DNAs (Bivalvia Mytilidae) BMC GENOMICS, 12:442.
  48. Breton S., Ghiselli F., Passamonti M., Milani L., Stewart D.T., Hoeh W. R. (2011) Evidence for a fourteenth mtDNA-encoded protein in the female-transmitted mtDNA of marine mussels (Bivalvia: Mytilidae). PLoS ONE, 6(4): e19365.
  49. Plazzi F., Ricci A., Passamonti M. (2011) The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of the orthopteroid insects. MOLECULAR PHYLOGENETICS AND EVOLUTION, 58: 304-316.
  50. Ghiselli F., Milani L., Passamonti M. (2011) Strict sex-specific mtDNA segregation in the germline of the DUI species Venerupis philippinarum (Bivalvia Veneridae). MOLECULAR BIOLOGY AND EVOLUTION, 28(2): 949-961.
  51. Plazzi F., Passamonti M. (2010) Towards a molecular phylogeny of mollusks: bivalves’ early evolution as revealed by mitochondrial genes. MOLECULAR PHYLOGENETICS AND EVOLUTION, 57(2): 641-657.
  52. Scali V., Milani L., Passamonti M. (2010) Clonopsis gallica, a stick insect parthenogen exploiting different egg maturation mechanisms over its range. INVERTEBRATE REPRODUCTION AND DEVELOPMENT, 54(3): 143-150.
  53. Demontis D., Pertoldi C., Passamonti M., Scali V. (2010) Increased fluctuating asymmetry in a naturally occurring hybrid zone between the stick insects Bacillus rossius rossius and Bacillus rossius redtenbacheri. JOURNAL OF INSECT SCIENCE, 10: 157.
  54. Milani L., Ghiselli F., Pellecchia M., Scali V., Passamonti M. (2010) Reticulate evolution in stick insects: the case of Clonopsis (Insecta Phasmida). BMC EVOLUTIONARY BIOLOGY, 10: 258.
  55. Plohl M., Petrovic V., Luchetti A., Ricci A., Satovic E., Passamonti M., Mantovani B. (2010) Long-term conservation vs high sequence divergence: the case of an extraordinary old satellite DNA in bivalve mollusks. HEREDITY, 104: 543-551.
  56. Guarniero I., Plazzi F., Rinaldi A., Trentini M., Passamonti M. (2010) Comparative analysis of four different genic loci in the bivalve mollusc Mactra corallina: genetic evidence of existing sibling species. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 9(3): 633-644.
  57. Plazzi F., Ferrucci R.R., Passamonti M. (2010) Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. BMC BIOINFORMATICS, 11:209.
  58. Milani L., Scali V., Passamonti M. (2009) The Clonopsis gallica puzzle: Mendelian species, polyploid parthenogens with karyotype re-diploidisation and clonal androgens in Moroccan stick insects. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH. Vol. 47(2): pp. 132-140.
  59. Passamonti M., F. Ghiselli. (2009) Doubly Uniparental Inheritance: two mitochondrial genomes, one precious model for organelle DNA inheritance and evolution. DNA AND CELL BIOLOGY. vol. 28(2), pp. 79-89.
  60. Ricci A., V. Scali, M. Passamonti. (2008). The IGS-ETS in Bacillus (Insecta Phasmida): molecular characterization and the relevance of sex in ribosomal DNA evolution. BMC EVOLUTIONARY BIOLOGY. vol. 8 (278), 1-11.
  61. Ghiselli F., L. Milani, V. Scali, M. Passamonti. (2007). The Leptynia hispanica species complex (Insecta Phasmida): polyploidy, parthenogenesis, hybridization and more. MOLECULAR ECOLOGY. vol. 16 (20), 4256-4268.
  62. Passamonti M. (2007). An unusual case of gender-associated mitochondrial DNA heteroplasmy: the mytilid Musculista senhousia (Mollusca Bivalvia). BMC EVOLUTIONARY BIOLOGY. vol. 7 (Suppl. 2).
  63. Passamonti M., Mantovani B., Scali V. (2004). Phylogeny and karyotype evolution of the Iberian Leptynia attenuata species complex (Insecta Phasmatodea). MOLECULAR PHYLOGENETICS AND EVOLUTION, 30: 87-96.
  64. Cesari M., Luchetti A., Passamonti M., Scali V., Mantovani B. (2003). Polymerase chain reaction of the Bag 320 satellite family reveals the ancestral library module and paleoconversion events in Bacillus rossius (Insecta Phasmatodea). GENE, 312: 289-295.
  65. Luchetti A., Cesari M., Carrara G., Cavicchi S., Passamonti M., Scali V., Mantovani B. (2003). Unisexuality and Molecular Drive: Bag320 Sequence Diversity in Bacillus Taxa (Insecta Phasmatodea). JOURNAL OF MOLECULAR EVOLUTION, 56: 587-596.
  66. Passamonti M., Boore J. L., Scali V. (2003). Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum. GENETICS 164:603-611.
  67. Scali V., Passamonti M., Marescalchi O., Mantovani B. (2003). Sex linkage to asexual lineages: genome evolution in Bacillus stick insects. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, 79: 137-150.
  68. Passamonti M., Scali V. (2001). Gender-associated mitochondrial DNA heteroplasmy in the venerid clam Tapes philippinarum (Mollusca Bivalvia). CURRENT GENETICS, 39: 117-124.
  69. Mantovani B., Passamonti M., Scali V. (2001). The mitochondrial cytochrome oxidase II gene in Bacillus stick-insects: ancestry of hybrids, androgenesis and phyletic relationships. MOLECULAR PHYLOGENETICS AND EVOLUTION 19: 157-163.
  70. Passamonti M., Mantovani B., Scali V. (2000). SDS-PAGE identification of raw and cooked clam species of the Veneridae family. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 80, 741-742.
  71. Passamonti M., Mantovani B., Scali V. (1999). Karyotype and allozyme characterization of the Iberian Leptynia attenuata species complex (Insecta Phasmatodea). ZOOLOGICAL SCIENCE, 16 (4), 675-684.
  72. Passamonti M., Mantovani B., Scali V. (1999). Allozymic analysis of some Mediterranean Veneridae (Mollusca: Bivalvia): preliminary notes on taxonomy and systematics of the family. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 79, 899-908.
  73. Mantovani B, Passamonti M, Scali V. (1999). Genomic evolution in parental and hybrid taxa of the genus Bacillus (Insecta Phasmatodea). ITALIAN JOURNAL OF ZOOLOGY, 66: 265-272.
  74. Passamonti M., Mantovani B., Scali V. (1998). Characterization of a highly repeated DNA family in Tapetinae species (Mollusca Bivalvia: Veneridae). ZOOLOGICAL SCIENCE, 15, 599-605.
  75. Passamonti M., Mantovani B., Scali V., Froglia C. (1997). Genetic Differentiation of European Species of Liocarcinus (Crustacea: Portunidae): a Gene-Enzyme Study. ZOOLOGISCHER ANZEIGER, 235 (3-4): 157-164.
  76. Passamonti M., Mantovani B., Scali V., Froglia C. (1997). Allozymic Characterization of Scottish and Aegean populations of Nephrops norvegicus. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, 77, 727-735.
  77. Passamonti M., Mantovani B., Scali V. (1997). Allozymic Characterization and Genetic Relationships among Four Species of Tapetinae (Bivalvia Veneridae). ITALIAN JOURNAL OF ZOOLOGY, 64 (2): 117-124.