MARIA BONITO

Dottoressa di ricerca

ciclo: XXXIII



Titolo della tesi: ANALYSIS OF NON-ALLELIC GENE CONVERSION IN THE EVOLUTION OF HUMAN MSY PALINDROMES

The Male-Specific region of Y chromosome (MSY) has long been considered a recombinationally inert genomic element, a view that has been profoundly dismissed by the discovery that the sequence landscape of this region can be actually modulated by inter- and intra- chromosomal recombination. The MSY includes eight large near-identical inverted repeats, palindromes P1-P8, considered to be in a ‘pseudo-diploid’ state. Although these structures originated in a non-recombining context, they evolved a strong self-recombinational activity in the form of non-allelic gene conversion, by which their arm-to-arm similarity exceeds 99.9%. Palindromic sequences contain many genes essential for sperm production and evolved independently on the constitutively haploid sex chromosomes of several taxa. Thus, it has been hypothesised that gene conversion is a mechanism necessary to counteract new possibly deleterious variants by retaining the ancestral state of gene sequences, in order to preserve their functionality over time. This hypothetical bias towards the retention of the ancestral state has also been proposed to explain the lower human-chimpanzee sequence divergence in the palindrome arms compared to palindrome spacers. However, despite the relevance of this mechanism in maintaining genome integrity, it is not clear if the bias towards the ancestral state really exists and little is known about the dynamics of gene conversion in the ampliconic MSY. Moreover, it is still unknown if differences in the conversion dynamics of different palindromes exist. To shed light on these issues, we performed a high-depth (>50×) targeted next-generation sequencing (NGS) of palindromes P6, P7 and P8 in 157 samples, which cover the most divergent evolutionary lineages of the human Y chromosome. We reconstructed a stable Y phylogeny of samples to explore gene conversion in an evolutionary context and found a large number of previously undescribed PSVs, increasing the possibility to identify gene conversion events occurring during the recent human history. By mapping these events across our phylogeny and comparing the sequences of the three palindromes conserved between human and chimpanzee, we were able to infer the minimum number of conversions, palindrome-specific mutation and gene conversion rates and the direction of the gene conversion mechanism (ancestral/derived, GC-bias). We found no evidences for a bias towards the retention of the ancestral state and that the evolution of different palindromes is governed by independent and complex dynamics. We also observed higher mutation rates in the spacers compared to palindrome arms that may represent the true cause of the previously observed higher human-chimpanzee spacer divergence with respect to the arms, without the need to invoke a Y-Y recombination bias towards the ancestral state.

Produzione scientifica

11573/1693293 - 2023 - The genomic echoes of the last Green Sahara on the Fulani and Sahelian people
D'atanasio, Eugenia; Risi, Flavia; Ravasini, Francesco; Montinaro, Francesco; Hajiesmaeil, Mogge; Bonucci, Biancamaria; Pistacchia, Letizia; Amoako-Sakyi, Daniel; Bonito, Maria; Onidi, Sara; Colombo, Giulia; Semino, Ornella; Destro Bisol, Giovanni; Anagnostou, Paolo; Metspalu, Mait; Tambets, Kristiina; Trombetta, Beniamino; Cruciani, Fulvio - 01a Articolo in rivista
rivista: CURRENT BIOLOGY (Current Biology Limited:84 Theobalds Road, London WC1X 8RR United Kingdom:011 44 20 76114202, EMAIL: info@biomednet.com, INTERNET: http://www.biomednet.com, Fax: 011 44 20 76114479) pp. - - issn: 0960-9822 - wos: WOS:001141295800001 (0) - scopus: (0)

11573/1655146 - 2022 - Disclosing complex mutational dynamics at a Y chromosome palindrome evolving through intra- and inter-chromosomal gene conversion
Bonito, Maria; Ravasini, Francesco; Novelletto, Andrea; D'atanasio, Eugenia; Cruciani, Fulvio; Trombetta, Beniamino - 01a Articolo in rivista
rivista: HUMAN MOLECULAR GENETICS (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485) pp. - - issn: 0964-6906 - wos: WOS:000844565400001 (1) - scopus: 2-s2.0-85146364587 (1)

11573/1583977 - 2021 - New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion
Bonito, Maria; D'atanasio, Eugenia; Ravasini, Francesco; Cariati, Selene; Finocchio, Andrea; Novelletto, Andrea; Trombetta, Beniamino; Cruciani, Fulvio - 01a Articolo in rivista
rivista: HUMAN MOLECULAR GENETICS (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485) pp. - - issn: 0964-6906 - wos: WOS:000728178600006 (5) - scopus: 2-s2.0-85121103171 (5)

11573/1583840 - 2021 - Identification and molecular characterisation of an unusually short allele at the SE33 (ACTBP2) locus resulting in a putative tri-allelic pattern at a flanking marker
Bonito, Maria; D'atanasio, Eugenia; Trombetta, Beniamino; Cannone, Francesco; Berti, Andrea; Cruciani, Fulvio - 01f Lettera, Nota
rivista: FORENSIC SCIENCE INTERNATIONAL. GENETICS (Amsterdam : Elsevier B.V.) pp. - - issn: 1878-0326 - wos: WOS:000691184500001 (1) - scopus: 2-s2.0-85106560208 (2)

11573/1549652 - 2021 - Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication
Ravasini, F.; D'atanasio, E.; Bonito, M.; Bonucci, B.; Della Rocca, C.; Berti, A.; Trombetta, B.; Cruciani, F. - 01a Articolo in rivista
rivista: FRONTIERS IN GENETICS (Lausanne : Frontiers Research Foundation, 2010-) pp. 1-8 - issn: 1664-8021 - wos: WOS:000645544300001 (6) - scopus: 2-s2.0-85105192457 (6)

11573/1679178 - 2021 - History and evolution of the Picene Culture through Ancient DNA analysis
Ravasini, Francesco; Bonito, Maria; Delpino, Chiara; Finocchi, Stefano; Giroldini, Pierluigi; Cilli, Elisabetta; Scheib Christiana, Lyn; Cruciani, Fulvio; D'atanasio, Eugenia; Trombetta, Beniamino - 04f Poster
congresso: Human Evolution - From Fossils to Ancient and Modern Genomes, Wellcome Connecting Science (Online)
libro: Human Evolution - From Fossils to Ancient and Modern Genomes - ()

11573/1441893 - 2020 - Y haplogroup diversity of the Dominican Republic. Reconstructing the effect of the European colonization and the trans-Atlantic slave trades
D'atanasio, Eugenia; Trionfetti, Flavia; Bonito, Maria; Sellitto, Daniele; Coppa, Alfredo; Berti, Andrea; Trombetta, Beniamino; Cruciani, Fulvio - 01a Articolo in rivista
rivista: GENOME BIOLOGY AND EVOLUTION (Oxford : Oxford University Press) pp. 1579-1590 - issn: 1759-6653 - wos: WOS:000599652200008 (4) - scopus: 2-s2.0-85092332074 (4)

11573/1441887 - 2020 - Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel
Della Rocca, C.; Cannone, F.; D'atanasio, E.; Bonito, M.; Anagnostou, P.; Russo, G.; Barni, F.; Alladio, E.; Destro-Bisol, G.; Trombetta, B.; Berti, A.; Cruciani, F. - 01a Articolo in rivista
rivista: FORENSIC SCIENCE INTERNATIONAL: GENETICS (Elsevier) pp. 1-9 - issn: 1872-4973 - wos: WOS:000587824500012 (7) - scopus: 2-s2.0-85090049481 (9)

11573/1340011 - 2019 - Dynamics of gene conversion in human MSY palindromes
Bonito, Maria; D'atanasio, E.; Novelletto, A.; Cruciani, F.; Trombetta, B. - 04f Poster
congresso: SMBE (Manchester)
libro: SMBE 2019 - ()

11573/1187393 - 2019 - Identification and molecular characterisation of an AMEL-X null allele due to an Alu insertion
D’Atanasio, Eugenia; Bonito, Maria; Iacovacci, Giuseppe; Berti, Andrea; Trombetta, Beniamino; Cruciani, Fulvio - 01i Case report
rivista: FORENSIC SCIENCE INTERNATIONAL: GENETICS (Elsevier) pp. - - issn: 1872-4973 - wos: WOS:000451726600001 (2) - scopus: 2-s2.0-85057341050 (2)

11573/1187215 - 2019 - Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa
D'atanasio, Eugenia; Iacovacci, Giuseppe; Pistillo, Rossella; Bonito, Maria; Dugoujon, Jean-Michel; Moral, Pedro; El-Chennawi, Farha; Melhaoui, Mohammed; Baali, Abdellatif; Cherkaoui, Mohamed; Sellitto, Daniele; Trombetta, Beniamino; Berti, Andrea; Cruciani, Fulvio - 01a Articolo in rivista
rivista: FORENSIC SCIENCE INTERNATIONAL: GENETICS (Elsevier) pp. 185-194 - issn: 1872-4973 - wos: WOS:000451726600027 (23) - scopus: 2-s2.0-85056249214 (25)

11573/1121352 - 2018 - Genetic diversity at three palindromic sequences of the human Y chromosome
Bonito, M; D’Atanasio, E; Novelletto, A; Cruciani, F; Trombetta, Beniamino - 04d Abstract in atti di convegno
congresso: 11th Haploid Markers Conference InferrIng Ancestry from DnA (Bydgoszcz, Poland)
libro: 11th Haploid Markers Conference InferrIng Ancestry from DnA - ()

11573/1205346 - 2018 - Dynamics of gene conversion in human Y-chromosome palindromes
Bonito, Maria; D'atanasio, E.; Novelletto, A.; Cruciani, F.; Trombetta, B. - 04f Poster
congresso: XV FISV Congress (Roma (Italy))
libro: XV FISV CONGRESS Programme and Abstracts - ()

11573/1121488 - 2018 - IDENTIFICATION AND MOLECULAR CHARACTERISATION OF AN AMEL-X NULL ALLELE DUE TO AN ALU INSERTION.
D'atanasio, Eugenia; Bonito, Maria; Iacovacci, Giuseppe; Berti, Andrea; Trombetta, Beniamino; Cruciani, Fulvio - 04f Poster
congresso: Human Identification Solutions (HIDS) (ROMA, Italia)
libro: Human Identification Solutions (HIDS) - ()

11573/1121374 - 2018 - Rapidly mutating Y-STRs in rapidly expanding populations: discrimination power of the Yfiler Plus multiplex in northern Africa.
D'atanasio, Eugenia; Iacovacci, G; Pistillo, R; Bonito, M; Dugoujon, Jm; Moral, P; El-Chennawi, F; Sellitto, D; Trombetta, B; Berti, A; Cruciani, F - 04d Abstract in atti di convegno
congresso: 11th Haploid Markers Conference InferrIng Ancestry from DNA (Bydgoszcz, Poland)
libro: 11th Haploid Markers Conference InferrIng Ancestry from DNA - ()

11573/1121467 - 2018 - Rapidly mutating Y-STRs in rapidly expanding populations:discrimination power of the Yfiler Plus multiplex in northern Africa.
D'atanasio, Eugenia; Iacovacci, Giuseppe; Pistillo, Rossella; Bonito, Maria; Dugoujon, Jean-Michel; Moral, Pedro; El-Chennawi, Farha; Sellitto, Daniele; Trombetta, Beniamino; Berti, Andrea; Cruciani, Fulvio - 04f Poster
congresso: Human Identification Solutions (HIDS) (ROMA, Italia)
libro: Human Identification Solutions (HIDS) - ()

11573/1068014 - 2018 - The peopling of the last green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages
D'atanasio, Eugenia; Trombetta, Beniamino; Bonito, Maria; Finocchio, Andrea; Di Vito, Genny; Seghizzi, Mara; Romano, Rita; Russo, Gianluca; Paganotti, Giacomo Maria; Watson, Elizabeth; Coppa, Alfredo; Anagnostou, Paolo; Dugoujon, Jean-Michel; Moral, Pedro; Sellitto, Daniele; Novelletto, Andrea; Cruciani, Fulvio - 01a Articolo in rivista
rivista: GENOME BIOLOGY (BioMed Central) pp. 1-15 - issn: 1474-760X - wos: WOS:000425109700001 (31) - scopus: 2-s2.0-85041958280 (35)

11573/1121548 - 2017 - Holocene human migrations in Africa: a male perspective
D'atanasio, Eugenia; Trombetta, Beniamino; Bonito, Maria; Coppa, Alfredo; Destro-Bisol, Giovanni; Dugoujon, Jean-Michel; Moral, Pedro; Sellitto, Daniele; Novelletto, Andrea; Cruciani, Fulvio - 04d Abstract in atti di convegno
congresso: Congresso AGI 2017 – Celebrating 60 years of the Italian Association of Genetics (Cortona, Italia)
libro: Congresso AGI 2017 – Celebrating 60 years of the Italian Association of Genetics - ()

11573/1121336 - 2016 - Human Y chromosome diversity and the peopling of the “Green Sahara” during the Holocene humid phase
D’Atanasio, E.; Di Vito, G.; Seghizzi, M.; Sellitto, D.; Bonito, Maria; Catino, G.; Pistillo, R.; Moral, P.; Dugoujon, J. M.; Russo, G.; Novelletto, A.; Trombetta, B.; Cruciani, F. - 04d Abstract in atti di convegno
congresso: FISV 2016 XIV Congress (ROMA, Italia)
libro: Program and Abstracts of the XIV FISV CONGRESS - ()

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