Dr Anneri Lötter

As a child I have always wanted to work in a laboratory. Although at that stage I had no knowledge of what that entailed, as I grew up and gathered more information, my interest in the field of biological sciences grew. It was only when I started my undergraduate degree that I was exposed to the various fields of biology. I find biology awe-inspiring, but I also found it striking that we knew so little. The fact remains that we know more about the moon than we know about our own planet, and the systems that drive it. I did my undergraduate degree in Medical Science and my BScHons degree in Genetics. My BScHons project focused on using SNP markers to map the ancestry and the parental species from which chromosomal segments originate within second generation hybrids of Eucalyptus grandis andE. nitens. My BScHons project exposed me to the field of molecular breeding and specifically how some annual crop breeding programs are far more advanced than those used for tree improvement. In order to further explore if such advanced breeding strategies can be implemented I decided to continue with an MSc in Genetics. My MSc project was focused on assembly of phased reference genomes for two Eucalyptusspecies using a trio-binning approach. During my MSc I went on a research visit to the University of Connecticut to improve my genome assembly bioinformatics skills.

Currently, my PhD project is focused on understanding how structural variation and transposable elements contribute to gene diversity, gene expression and phenotypic diversity observed in E. grandis. My personal aim is to further improve understanding of how haplotype and structural variants contribute to gene expression and the resulting phenotype in Eucalyptus, similar to recent studies in tomato.

INTERNATIONAL CONFERENCES

Anneri Lötter, Tuan A. Duong, John T. Lovell, Jane Grimwood, Jerry W. Jenkins, Tomas Bruna, Kerrie Barry, Jayson Talag, Jeremy Schmutz, Jill L. Wegrzyn and & Alexander A. Myburg, The pan-genome of Eucalyptus grandis, 12 – 17 January 2024, Plant and Animal Genome XXVIII Conference, San Diego, California, USA (Oral presentation).

Anneri Lötter, Nganeavhutshilo Nangammbi, Tuan A. Duong, Jane Grimwood, Tomas Bruna, Kerrie Barry, Jayson Talag, Jerry W. Jenkins, John T. Lovell, Jeremy Schmutz, Justin Borevitz, Jill L. Wegrzyn and & Alexander A. Myburg, Pan-genome and population sequencing of Eucalyptus grandis - a woody biomass crop, 12 – 17 January 2024, Plant and Animal Genome XXVIII Conference, San Diego, California, USA (Oral presentation).

Anneri Lötter, Tuan A. Duong, Julia Candotti, Eshchar Mizrachi, Jill L. Wegrzyn, Alexander A. Myburg, Structural variation in the haplogenomes of an F1 hybrid ofEucalyptus urophylla and E. grandis, 07 – 09 July 2022, 2022 IUFRO / Forest Tree Molecular Biology and Biotechnology (FTMB) Conference, Harbin, China (Online poster presentation).

Alexander A. Myburg, Julia Candotti, Anneri Lötter, Melissa Reynolds, Nanette Christie, Marja M. Mostert-O’Neill, A pan-genome view of complex trait dissection in Eucalyptus, 07 - 10 June 2022, Population, Evolutionary, and Quantitative Genetics Conference (PEQG2022), Pacific Grove, California, USA (Online poster presentation, co-author).

Anneri Lötter, Julia Candotti, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Structural variant discovery in haplotype resolved genomes of Eucalyptus grandis and E. urophylla, 19 - 23 July, Plant Biology 2021 Worldwide Summit (Online poster presentation).

Julia Candotti, Anneri Lötter, Marja M. O’Neill, S. Melissa Reynolds, Nanette Christie, Raphael Ployet, Gert van der Berg, Sharmane Naidoo, Nicoletta Jones, Sanushka Naidoo, Tuan A. Duong, Eshchar Mizrachi and Alexander A. Myburg, Towards understanding haplotype and structural variant diversity for Eucalyptus hybrid breeding, 19 - 23 July, Plant Biology 2021 Worldwide Summit (Online poster presentation, co-author).

Anneri Lötter, Tuan A. Duong, Julia Candotti, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Phased assembly of an F1 Eucalyptus urophylla x E. grandis hybrid genome using trio-binning approach, 17 -21 July, Plant Biology 2020 Worldwide Summit (Online poster presentation).

Anneri Lötter, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Sequencing and Phased Assembly of an Eucalyptus urophylla x E. grandis F1 Hybrid and Parental Genomes, 11 – 15 January 2020, Plant and Animal Genome XXVIII Conference, San Diego, California, USA (Poster presentation).

Anneri Lötter, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Sequencing and Phased Assembly of an Eucalyptus urophylla x E. grandis F1 Hybrid and Parental Genomes, 11 – 15 January 2020, Plant and Animal Genome XXVIII Conference, San Diego, California, USA (Poster presentation).

Anneri Lötter, J. Stephan Henning, Stephan Engelbrecht, Marja M. O’Neill, S. Melissa Reynolds, M. Mmoledi Mphahlele, Kitt G. Payn, Alexander A. Myburg, Local ancestry mapping in advanced generation Eucalyptus grandis X E. nitens hybrids, 24 – 28 June 2019, IUFRO Tree Biotechnology 2019 Meeting, Raleigh, North Carolina, USA (Poster presentation, co-author).

S. Melissa Reynolds, J. Stephan Henning, Anneri Lötter, Stephan Engelbrecht, Marja O’Neill, M. Mmoledi Mphahlele, Steve D. Verryn, Kitt G. Payn, Nicoletta Jones, Arnulf Kanzler, Alexander A. Myburg, Establishing a genome diversity atlas for Eucalyptus and its applications to molecular breeding in advanced generation interspecific hybrids, 18 – 21 February 2019, Hobart, Tasmania, Australia (Poster presentation, co-author).NATIONAL CONFERENCES

Alexander A. Myburg, Anneri Lötter, Nhlanhla Simelane, Aspen Downing, Kelebogile Happy Sathekge, Nanette Christie, Tuan A. Duong, Marja Mostert-O’Neill, Oluwaseun Gakenou, David Drew, Jill L. Wegrzyn, High-throughput genome sequencing in the natural range of Eucalyptus grandis – restarting the domestication and breeding of an iconic South African forestry species, 26-27 November 2024, Forestry Science Symposium, Hilton, South Africa (Oral presentation, co-author).

Anneri Lötter, Genome phasing, annotation and variant calling, 12 November 2024, UPGL (University of Pretoria Genomics Laboratory) NGS Project Planning Workshop, Pretoria, South Africa (Oral presentation).

Anneri Lötter, Tuan A. Duong, Jane Grimwood, Tomas Bruna, Kerrie Barry, Jayson Talag, Jerry W. Jenkins, John T. Lovell, Jeremy Schmutz, Justin Borevitz, Jill L. Wegrzyn, Alexander A. Myburg, The pan-genome of Eucalyptus grandis, 23 – 25 September 2024, South African Genetics Society and South African Society for Bioinformatics: BIO2024, Pretoria, South Africa (Oral presentation).

Anneri Lötter, Nhlanhla Simelane, Aspen Downing, Kelebogile Happy Sathekge, Nanette Christie, Tuan A. Duong, Marja Mostert-O’Neill, Oluwaseun Gakenou, David Drew, Jane Grimwood, Tomas Bruna, Kerrie Barry, Jayson Talag, Adam Healey, Jerry W. Jenkins, John T. Lovell, Jeremy Schmutz, Justin Borevitz, Jill L. Wegrzyn, Alexander A. Myburg, Reference, pan- and population genome sequencing of the eucalypts for woody biomass and adaptive traits, 23 – 25 September 2024, South African Genetics Society and South African Society for Bioinformatics: BIO2024, Pretoria, South Africa (Oral presentation, co-author).

Aspen Downing, Anneri Lötter, Nanette Christie, Alexander A. Myburg, Isoform diversity in Eucalyptus grandis, 23 – 25 September 2024, South African Genetics Society and South African Society for Bioinformatics: BIO2024, Pretoria, South Africa (Poster presentation, co-author).

Monique H. Maartens, Mary Ranketse, Anneri Lötter, Nadine Kleinhans, Tuan A. Duong, Nanette Christie, Jill L. Wegrzyn, Alexander A. Myburg, Sequencing the gene space of tropical pine trees, 23 – 25 September 2024, South African Genetics Society and South African Society for Bioinformatics: BIO2024, Pretoria, South Africa (Poster presentation, co-author).

Aspen Downing, Anneri Lötter, Nanette Christie, Alexander A. Myburg, Isoform diversity in Eucalyptus grandis, 22 September 2024, South African Genetics Society and South African Society for Bioinformatics: BIO2024 student symposium, Pretoria, South Africa (Oral presentation, co-author).

Anneri Lötter, Genome phasing, annotation and variant calling, 05 July 2024, UPGL Next Generation Sequencing Information Day 2024, Pretoria, South Africa (Oral presentation).

Anneri Lötter, Julia Candotti, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn, Alexander A. Myburg, Phased genome assembly of Eucalyptus tree genomes: unravelling sequence and structural variation in a highly outbred crop, 21 October 2022, Nanopore Day Johannesburg 2022, Johannesburg, South Africa (Oral presentation).

Anneri Lötter, Julia Candotti, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Phased genome assembly and haplogenome comparison in an F1 hybrid of Eucalyptus urophylla and E. grandis, 24 – 27 April 2022, South African Genetics Society and South African Society for Bioinformatics: BIO2022, Western Cape, South Africa (Oral presentation).

Anneri Lötter, Julia Candotti, Tuan A. Duong, Eshchar Mizrachi, Jill L. Wegrzyn and Alexander A. Myburg, Towards haplotype-based genomic breeding: Phased assembly of a Eucalyptus urophylla x E. grandis F1 hybrid genome, 08 – 11 March 2020, 13th Southern African Plant Breeding Symposium 2020, Pretoria, South Africa (Speed talk).

Dr Anneri Lötter

Dr Anneri Lötter

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My Publications