Genomics and transcriptomics

Recent publications

1. E Krzywinska, P Ribeca, L Ferretti, A Hammond and J Krzywinski, “A novel factor modulating X chromosome dosage compensation in Anopheles”, Current Biology (2023).

2. E Krzywinska, L Ferretti and J Krzywinski, “A male-specific cell line from the African malaria mosquito Anopheles gambiae: Establishment and a comparative transcriptomic analysis”, Scientific Reports (2022).

3. E Krzywinska, L Ferretti, J Li, J-C Li, C-H Chen and J Krzywinski “femaleless controls sex determination and dosage compensation pathways in females of Anopheles mosquitoes”, Current Biology 31 1084–1091 (2021).

4. A Jadhav, L Zhao, A Ledda, W Liu, C Ding, V Nair and L Ferretti, “Patterns of RNA editing in Newcastle Disease Virus infections”, Viruses 12 1249 (2020).

5. Ferretti L, Kraemer-Eis A and Schiffer P, “Conserved patterns in developmental processes and phases, rather than genes, unite the highly divergent Bilateria”, Life 10 (9), 182 (2020).

6. Ferretti L, Tennakoon C, Silesian A, Freimanis G and Ribeca P, “SiNPle: fast and sensitive variant calling for deep sequencing data”, Genes 10 (8):561 (2019).

Genetic mechanisms of sex determination and dosage balance in insects 

• We studied the allelic variability in the hypervariable complementary sex determination (csd) locus in Apis mellifera [1]. We found conditions for functional heterozygotes, based on minimum aminoacid and length diversity, and we showed that negative-frequency selection generated a large number of functionally different alleles (about 150 worldwide and 100 in Kenya only). We also studied the mechanisms of dosage compensation of sexual chromosomes during the development of Anopheles gambiae [2]. The expression of the X chromosome is (fully or partially) dosage compensated in larvae and pupae. 

  1. Lechner S, Ferretti L, Schöning C, Kinuthia W, Willemsen D and Hasselmann M, Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honeybee Apis mellifera, Mol. Biol. Evol. 31 (2) 272-287 (2013).

  2. Rose G, Krzywinska E, Kim J, Revuelta L, Ferretti L and Krzywinski J, “Dosage compensation in the African malaria mosquito Anopheles gambiae”, Genome Biology and Evolution, 8 (2): 411-425 (2016). 

Methods for population genetics from Next Generation Sequencing data

• We developed several methods for NGS data. We extended neutrality tests like Tajima's D and Fay and Wu's H to NGS data, both using called sequences with missing data and correcting for missing information [3]. We presented a general framework for Watterson estimators of variability from all kinds of NGS data, including haploid and diploid individuals, trios, pools and polyploids [2] as well as a general analysis of the frequency spectrum in autopolyploids [7]. For pooled data, we developed a Bayesian SNP caller using the neutral frequency spectrum as a prior [4] and proposed a Maximum Composite Likelihood estimator of variability and a complete set of tests: Tajima's D, Fay and Wu's H, HKA etc, specific for pooled NGS samples [1]. We also wrote a recent review on population genomics methods for neglected genomes, focused on arthropods [5] and a (slightly outdated) review on the methods and applications of NGS for animal genetics, containing some material on pool sequencing [6].

  1. Ferretti L, Ramos-Onsins SE and Perez-Enciso M, Population genomics from pool sequencing, Molecular Ecology (2013), 22: 5561-5576.

  2. Ferretti L and Ramos-Onsins SE, Watterson estimators for Next Generation Sequencing: from trios to autopolyploids, Theor Popul Biol. 100C:79-87 (2015). arXiv.

  3. Ferretti L*, Raineri E* and Ramos-Onsins SE, Neutrality tests for sequences with missing data, Genetics 191(4):1397-401 (2012).

  4. Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S and Perez-Enciso M, SNP calling by sequencing pooled samples, BMC Bioinformatics 13:239 (2012).

  5. Hasselmann M, Ferretti L and Zayed A, “Beyond fruit-flies: Population genomic advances in non-dipteran arthropods”, Briefings in Functional Genomics, 14 (6): 424-431 (2015). 

  6. Perez-Enciso M and Ferretti L, Massive parallel sequencing in animal genetics: wherefroms and wheretos, Anim Genet. 41(6):561-9 (2010).

  7. Ferretti L, Ribeca P and Ramos-Onsins SE, "The Site Frequency/Dosage Spectrum of autopolyploid populations", Frontiers in Genetics (2018).

Evolution of recombination in mammals

• We studied the evolution of the recombination rate, number of crossovers etc. in several species of mammals [1]. Recombination rates increase over time and their evolution appears to be punctuated and subject to selection. Another interesting observation is the high recombination rate and the strangely weak crossover interference in the tiger.

  1. Segura J, Ferretti L, Ramos-Onsins S, Capilla L, Farre M, Reis F, Oliver-Bonet M, Fernandez-Bellon H, Garcia F, Garcia-Caldes M, Robinson T, Ruiz-Herrera A, Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference, Proceedings of the Royal Society B, 280 1771 1471-2954 (2013).

Swine evolution and domestication

• We applied the methods developed for pooled NGS data to variability and differentiation in wild boar and international pig breeds, in order to infer which genes and functions were targets of artificial selection during domestication [3]. We studied the patterns of variability in a single Iberian pig [2] and in pooled data from an Iberian pig population [1].

  1. Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silio L, Rodriguez MC, Groenen MA, Ramos-Onsins SE, Perez-Enciso M, Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs, BMC Genomics. 2013 Mar 5;14:148.

  2. Esteve-Codina A, Kofler R, Himmelbauer H, Ferretti L, Vivancos AP, Groenen MA, Folch JM, Rodriguez MC, Perez-Enciso M, Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof, Heredity 107(3):256-64 (2011).

  3. Amaral AJ, Ferretti L, Megens HJ, Crooijmans RP, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MA, Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA, PLoS One 6(4):e14782 (2011). PLoS One.