After two years of online meetings due to COVID-19, the sixth Camelids Genomics Workshop at PAG XXX 2023 was organized by Felipe F Avila (Chair) and Gustavo Gutierrez (Co-chair)
PAG XXX, 2023; 6th Camelids Workshop
***********************
Workshop summary
***********************
Date: January 15th (1:30pm-3:40am)
Location: Town and Country Resort, room Palm 7 – San Diego, CA (USA)
Organizers
Chair: Dr. Felipe Avila, University of California – Davis (ffavila@ucdavis.edu)
Co-Chair: Dr. Gustavo Gutierrez, UNALM – Peru (gustavogr@lamolina.edu.pe)
Number of Participants: 34 participants from 24 different institutions worldwide. Their information was added to the PAG camelid workshop contact list (attached).
Summary:
This was the first in-person PAG meeting since 2020 due to the COVID-19 pandemic. Seven abstracts were accepted for oral presentation during the camelid workshop. All presenters delivered 12-minute talks followed by 3 minutes at the end for Q&A; at the end of the workshop, 15 minutes were reserved for discussions. The talks were split between New World (2) and Old World (5) camelids.
Workshop Presentations:
Unfortunately, due to the excellent seminars presented during the workshop, we did not have much time for discussion. We started by discussing the most pressing needs of the camelid genetics and genomics community: collaborations and funding. The necessity of an improved alpaca reference genome was also discussed (Dr. Terje Raudsepp, Texas A&M University), mainly as a means for inclusion of the alpaca in FAANG. Dr. Samantha Brooks (University of Florida) explained that a Multi-State was just funded for the horse genomics community, which will replace in part the funding that had been obtained through NRSP-8. She encouraged the camelid research community to seek out support from industry stakeholders, and by writing a collaborative, exciting application along the same lines of the equine Multi-State. The caveat would be that this proposal would only provide funding for our US-based researchers. Dr. Brian Davis (Texas A&M University) offered to call variants on any individuals with available WGS data as part of his group’s efforts to create a variant database for camelids. He said that he has established a pipeline to perform quality control and analyze WGS data and would be willing to do it for any camelid researcher that needed it.
Next Workshop Co-Chair:
This year’s co-chair, Dr. Gustavo Gutierrez, will serve as the Chair at PAG31 (2024). Dr. Hasan Al-Haddad (Kuwait University) was selected as co-chair for the camelid workshop next year.
=========================================================================================================================
=========================================================================================================================
The third cameldis Genomic Workshop at PAG XXVI 2018 was organized by Pamela Burger (Chair) and Don Miller (Co-Chair).
PAG XXVI, 2018; 3rd Camelids Workshop January 13
***********************
Workshop summary
**********************
Chair: Pamela Burger (Vetmeduni Vienna, Austria); Co-chair: Don Miller (Cornell University, USA)
Many thanks to all speakers and participants, who contributed to the third camelid workshop to make it a great success. We had a headcount of 46 people attending the workshop, and we were able to add 23 additional persons from 16 different institutions to the PAG camelid workshop contact list:
https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
During the selection process of the speakers we intended a good representation of the three Old World camel species in the presentation list. However, due to visa issues two young Chinese colleagues scheduled with their presentations about Bactrian camel gut microbiome and effects of Bactrian camel milk were not able to come, and we had to replace their talks. Unfortunately, our first speaker from Sharjah University did not manage to attend the conference.
Instead, Pamela Burger presented a short youtube info video on dromedary domestication from a science communication project “CamelSciencePub”. Afterwards, SAMANTHA BROOKS from University of Florida gave a summary about the activities and efforts to add Camelids to the National Animal Genome Research Project with the possibility to get separate funding opportunities. Furthermore, the negotiation with GeneSeek for a 80K SNP chip for dromedaries are ongoing, and she encouraged the workshop participants to add further specific SNPs from previous work. Also, Bactrian camel and Alpaca SNPs could be included in the SNP chip.
****************************
Workshop presentations
****************************
*) HEATHER HOLL from University of Florida presented about the de novo hybrid (Illumina, Pacbio, 10XGenomics) assmebly of dromedary genome, including reference assisted chromosome assembly (RACA) using Bos taurus genome and alpaca RH map.
*) FAHAD ALSHANBARI from Texas A&M University presented a candidate gene approach for causative mutations for the coat colours white and black, as well a pooled genome sequencing approach to identify genes associated with red colour phenotype.
*) MATT JEVIT from Texas A&M University presented an overview about the Y chromosome assembly and gene catalogue in Alpaca using flow-sorting and sequencing of the Y chromosome.
*) PAMELA BURGER from Vetmeduni Vienna replacing BARBARA WALLNER as speaker, presented a mapping and filtering approach for a de novo assembly of Y-chromosome specific contigs and identification of polymorphism to study male genealogies in Old World camels.
********************************
Workshop general discussion
********************************
The general discussion mainly was about how to integrate camelids as livestock species into the National Animal Genome Research Project (NRSP8) for increased funding possibilities. The major critics and refusal from NRSP side to integrate camelids is the monetary relevance of these species for the USA. Counter arguments would be to highlight camelids as specific and valuable resources for global food security. Also, the fibre market of alpaca is getting stronger.
More contributions (talks, proposals, discussion) to other established groups, either cattle/sheep/goat or horse were suggest to increase the visibility of camelids as important livestock species within the next 5 years, and then to submit again a proposal to the NRSP.
An update was made that the construction of an 80K SNP chip for dromedary, maybe also including alpaca and Bactrian camel SNPs is on the way with GeneSeek company. There is call to add geographically relevant samples and physiologically/ production relevant SNPs. Please send email to samantha.brooks@ufl.edu if you can contribute sequence data or SNP information.
*********************************
Next Workshop Chair election
*********************************
Don Miller is elected chair for the camelid workshop at PAGXXVII, 2019. As no co-chair for 2019 from the workshop participants was identified, we will ask Kylie Munyard (Curtin University, Australia, Alpaca genomics) if she agrees to become co-chair 2019/ chair for 2020.
===========================================================================================================================
===========================================================================================================================
The second Camelids Genomics Workshop at the PAG XXV was organized by Terje Raudsepp (Chair) and Pamela Burger (co-Chair).
PAG XXV, 2017; Camelids Workshop January 14
Summary
Many thanks to all speakers and participants for making the 2nd Camelids Workshop at PAG a success. According to the workshop registration sheet, the 2 h 10 min session had 33 participants from 22 institutions representing 11 countries Worldwide. However, headcount in the middle of the session reached 56.
Despite our good intentions to invite a keynote speaker for this workshop, the short time reserved for camelids did not allow this happen. In its current format, the workshop can host six-seven 15 min presentations and a brief discussion. Selection of talks for the 2017 workshop was species-driven and aimed to provide a representative coverage on genomics studies in both Old and New World species.
Workshop presentations
Heather Holl from the University of Florida opened the session with a talk on the status of a 53X Illumina and 20X PacBio hybrid assembly of the dromedary genome. Elena Ciani from the University of Bari, Italy, presented studies on dromedary populations from a wide geographic sampling: interestingly, none of the populations showed specific genetic structure, and populations in Kazakhstan and Iran indicated introgression with the Bactrian camel. Hussain Bahbahani from Kuwait University focused on whole genome sequence analysis of dromedaries selected for milk production or racing in the Arabian Peninsula. The only presentation on the genome of Bactrian camels was by Liang Ming from Inner Mongolia Agricultural University, China, and focused on the data obtained by resequencing-assembly of multiple Bactrian genomes for the development of genetic markers for both the domestic and wild populations. We learned that the wild Bactrian camel is more endangered than the Giant Panda. Mark Richardson from Deakin University, Australia, gave a progress report on the status of VicPac3.0 – an improved alpaca genome assembly achieved by incorporating 100X Illumina, 5X PacBio, and RNAseq data to the currently available VicPac2. The improved assembly is currently available at Deakin University server but the plan is to submit it to NCBI later in 2017. Felipe Avila from the University of Minnesota summarized the status of the cytogenetic map and integrated map data in camelids. To illustrate the application of molecular markers in camelid clinical cytogenetics, Felipe presented a case report of a sterile male llama carrying an autosomal translocation. The last talk was by Petr Hořín from the Brno Veterinary and Pharmaceutical University, Czech Republic, about sequence polymorphism of the MHC in Old World camelids.
Elections: Dr. Pamela Burger will serve as the Chair for PAG2018 Camelid Workshop with assistance from Dr. Don Miller (chair-elect for 2019).
Discussion (Panel: Samantha Brooks, Pamela Burger, Mark Richardson, Terje Raudsepp)
• FAANG: Possibility to include camelids in FAANG. Laura Clark from EMBL-EBI said that they can house data, either freely or hold until publication. She advised
to select tissues carefully, with the priority of high expression tissues, such as brain, testis, ovary. Suggested to avoid tissue overlap unless specific conditions of interest are identified. All in all, do as many tissues as possible and choose technology with long reads (iso-seq). Laura encouraged everyone continue with their current projects but advised to consider FAANG standards for the new ones. Importantly, we need to identify potential funding sources, e.g., national research foundations, Morris Animal Foundation, USDA?
• Phenotypes. Discussion about how and which camelid phenotypes to collect. Hasan Alhaddad from Kuwait University has made an iOS application “SamplEase” to facilitate sample collection in fieldwork settings. The app allows acquisition of basic data, including phtos. A recently EU funded project (Coordinator Prof. Juan Vicente Delgado Bermejo, University of Cordoba, Spain) is already collecting meat, milk and disease resistance phenotypes from dromedaries in Tunesia, Morocco, Algeria aiming for 2000 samples.
• Complex genomic regions and BAC library: in order to properly assemble complex genomic regions, for example, those harboring immunity related genes, a need for a dromedary genomic BAC library was discussed. Currently, the only BAC library in camelids is that of a female alpaca (CHORI-246). Questions: can alpaca BACs be used for sequence capture in the dromedary? Can 10X Genomics and Dovetail Genomics solve the assembly problems without BACs? Funding?
• Sweet dreams: Like everybody else, participants of the Camelid Workshop had great hopes that 10X Genomics and Dovetail Genomics will solve all their problems.
The day after:
• Sam Brooks brought a message from Jim Reecy that Animalgenome.org will be happy to host some large camelids datasets in their repository (we will get our own folder): http://www.animalgenome.org/repository/. Perhaps Mark Richardson et al would be interested to share the alpaca data there; Sam Brooks and Heather Holl will deposit a draft dromedary assembly.
• A small group (Pamela Burger, Doug Antczak, Petr Horin, Polina Perelman, Don Miller, Ernie Bailey and Terje Raudsepp) continued discussions about the best strategies for sequencing, assembly and study of immunity related genes (NK family) and MHC in camelids.
• Additional discussions (Polina Perelman, Mark Richardson, Denis Larkin, Pamela Burger, Terje Raudsepp) about publishing the alpaca 4000-marker RH map and its application to improve genome assembly. Also, discussions about sequencing clones from the recently constructed dromedary 5000rad and 15000rad RH panels – for improving dromedary sequence assembly and anchoring to chromosomes.
• Possibility to include camelids in NRSP8?
Finally and most importantly, in an effort to help us stay connected, last year Sam Brooks started a contact list for the workshop. The list is shared as a GoogleDoc and can be edited by anyone. Please feel free to correct your information and forward the link to whomever may wish to add themselves to the list. I already included new names from the 2017 workshop participants list.
Camelids Genome Workshop Contact List: https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
Once again, many, many thanks to all! Special thanks to Sam Brooks and Pamela Burger for taking meticulous notes during the workshop.
Have a happy and productive year 2017,
Terje
Terje Raudsepp, Ph.D; Associate Professor
Director of Molecular Cytogenetics Laboratory
Department of Veterinary Integrative Biosciences
College of Veterinary Medicine & Biomedical Sciences
Texas A&M University
488 Raymond Stotzer Pkw, VRB Room #314
PAG XXX, 2023; 6th Camelids Workshop
***********************
Workshop summary
***********************
Date: January 15th (1:30pm-3:40am)
Location: Town and Country Resort, room Palm 7 – San Diego, CA (USA)
Organizers
Chair: Dr. Felipe Avila, University of California – Davis (ffavila@ucdavis.edu)
Co-Chair: Dr. Gustavo Gutierrez, UNALM – Peru (gustavogr@lamolina.edu.pe)
Number of Participants: 34 participants from 24 different institutions worldwide. Their information was added to the PAG camelid workshop contact list (attached).
Summary:
This was the first in-person PAG meeting since 2020 due to the COVID-19 pandemic. Seven abstracts were accepted for oral presentation during the camelid workshop. All presenters delivered 12-minute talks followed by 3 minutes at the end for Q&A; at the end of the workshop, 15 minutes were reserved for discussions. The talks were split between New World (2) and Old World (5) camelids.
Workshop Presentations:
- Mayra Mendoza (PhD candidate, Texas A&M University): VicPac4, a chromosome-level reference genome of the alpaca (Vicugna pacos).
- Dr. Gustavo Gutierrez (Professor, UNALM – Peru): Evaluation of an Alpaca Genomic SNP Chip for Potential Use in North American Alpacas.
- Dr. Elena Ciani (Professor, University of Bari Aldo Moro): An extensive world-wide Camelus dromedarius genetic diversity study using whole-genome sequence data.
- Dr. Pamela Burger (Researcher, University of Veterinary Medicine Vienna, Austria): Conservation genomic monitoring for adaptation and introgressive hybridisation in the critically endangered wild camels (Camelus ferus) from Mongolia and China.
- Dr. Hasan Al-Haddad (Professor, Kuwait University): Coat phenotypes of dromedary camels and its current genetics.
- Panjiao Lin (PhD candidate, University of Bristol): Gene and Transcript-level Plasticity of the Core Hypothalamic Osmoregulatory Control Centre of the Arabian Dromedary Camel.
- Dr. Pamela Burger (Researcher, University of Veterinary Medicine Vienna, Austria): Importance of camelids in the COVID-19 pandemic and their immunogenetic response to coronavirus infection.
Unfortunately, due to the excellent seminars presented during the workshop, we did not have much time for discussion. We started by discussing the most pressing needs of the camelid genetics and genomics community: collaborations and funding. The necessity of an improved alpaca reference genome was also discussed (Dr. Terje Raudsepp, Texas A&M University), mainly as a means for inclusion of the alpaca in FAANG. Dr. Samantha Brooks (University of Florida) explained that a Multi-State was just funded for the horse genomics community, which will replace in part the funding that had been obtained through NRSP-8. She encouraged the camelid research community to seek out support from industry stakeholders, and by writing a collaborative, exciting application along the same lines of the equine Multi-State. The caveat would be that this proposal would only provide funding for our US-based researchers. Dr. Brian Davis (Texas A&M University) offered to call variants on any individuals with available WGS data as part of his group’s efforts to create a variant database for camelids. He said that he has established a pipeline to perform quality control and analyze WGS data and would be willing to do it for any camelid researcher that needed it.
Next Workshop Co-Chair:
This year’s co-chair, Dr. Gustavo Gutierrez, will serve as the Chair at PAG31 (2024). Dr. Hasan Al-Haddad (Kuwait University) was selected as co-chair for the camelid workshop next year.
=========================================================================================================================
=========================================================================================================================
The third cameldis Genomic Workshop at PAG XXVI 2018 was organized by Pamela Burger (Chair) and Don Miller (Co-Chair).
PAG XXVI, 2018; 3rd Camelids Workshop January 13
***********************
Workshop summary
**********************
Chair: Pamela Burger (Vetmeduni Vienna, Austria); Co-chair: Don Miller (Cornell University, USA)
Many thanks to all speakers and participants, who contributed to the third camelid workshop to make it a great success. We had a headcount of 46 people attending the workshop, and we were able to add 23 additional persons from 16 different institutions to the PAG camelid workshop contact list:
https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
During the selection process of the speakers we intended a good representation of the three Old World camel species in the presentation list. However, due to visa issues two young Chinese colleagues scheduled with their presentations about Bactrian camel gut microbiome and effects of Bactrian camel milk were not able to come, and we had to replace their talks. Unfortunately, our first speaker from Sharjah University did not manage to attend the conference.
Instead, Pamela Burger presented a short youtube info video on dromedary domestication from a science communication project “CamelSciencePub”. Afterwards, SAMANTHA BROOKS from University of Florida gave a summary about the activities and efforts to add Camelids to the National Animal Genome Research Project with the possibility to get separate funding opportunities. Furthermore, the negotiation with GeneSeek for a 80K SNP chip for dromedaries are ongoing, and she encouraged the workshop participants to add further specific SNPs from previous work. Also, Bactrian camel and Alpaca SNPs could be included in the SNP chip.
****************************
Workshop presentations
****************************
*) HEATHER HOLL from University of Florida presented about the de novo hybrid (Illumina, Pacbio, 10XGenomics) assmebly of dromedary genome, including reference assisted chromosome assembly (RACA) using Bos taurus genome and alpaca RH map.
*) FAHAD ALSHANBARI from Texas A&M University presented a candidate gene approach for causative mutations for the coat colours white and black, as well a pooled genome sequencing approach to identify genes associated with red colour phenotype.
*) MATT JEVIT from Texas A&M University presented an overview about the Y chromosome assembly and gene catalogue in Alpaca using flow-sorting and sequencing of the Y chromosome.
*) PAMELA BURGER from Vetmeduni Vienna replacing BARBARA WALLNER as speaker, presented a mapping and filtering approach for a de novo assembly of Y-chromosome specific contigs and identification of polymorphism to study male genealogies in Old World camels.
********************************
Workshop general discussion
********************************
The general discussion mainly was about how to integrate camelids as livestock species into the National Animal Genome Research Project (NRSP8) for increased funding possibilities. The major critics and refusal from NRSP side to integrate camelids is the monetary relevance of these species for the USA. Counter arguments would be to highlight camelids as specific and valuable resources for global food security. Also, the fibre market of alpaca is getting stronger.
More contributions (talks, proposals, discussion) to other established groups, either cattle/sheep/goat or horse were suggest to increase the visibility of camelids as important livestock species within the next 5 years, and then to submit again a proposal to the NRSP.
An update was made that the construction of an 80K SNP chip for dromedary, maybe also including alpaca and Bactrian camel SNPs is on the way with GeneSeek company. There is call to add geographically relevant samples and physiologically/ production relevant SNPs. Please send email to samantha.brooks@ufl.edu if you can contribute sequence data or SNP information.
*********************************
Next Workshop Chair election
*********************************
Don Miller is elected chair for the camelid workshop at PAGXXVII, 2019. As no co-chair for 2019 from the workshop participants was identified, we will ask Kylie Munyard (Curtin University, Australia, Alpaca genomics) if she agrees to become co-chair 2019/ chair for 2020.
===========================================================================================================================
===========================================================================================================================
The second Camelids Genomics Workshop at the PAG XXV was organized by Terje Raudsepp (Chair) and Pamela Burger (co-Chair).
PAG XXV, 2017; Camelids Workshop January 14
Summary
Many thanks to all speakers and participants for making the 2nd Camelids Workshop at PAG a success. According to the workshop registration sheet, the 2 h 10 min session had 33 participants from 22 institutions representing 11 countries Worldwide. However, headcount in the middle of the session reached 56.
Despite our good intentions to invite a keynote speaker for this workshop, the short time reserved for camelids did not allow this happen. In its current format, the workshop can host six-seven 15 min presentations and a brief discussion. Selection of talks for the 2017 workshop was species-driven and aimed to provide a representative coverage on genomics studies in both Old and New World species.
Workshop presentations
Heather Holl from the University of Florida opened the session with a talk on the status of a 53X Illumina and 20X PacBio hybrid assembly of the dromedary genome. Elena Ciani from the University of Bari, Italy, presented studies on dromedary populations from a wide geographic sampling: interestingly, none of the populations showed specific genetic structure, and populations in Kazakhstan and Iran indicated introgression with the Bactrian camel. Hussain Bahbahani from Kuwait University focused on whole genome sequence analysis of dromedaries selected for milk production or racing in the Arabian Peninsula. The only presentation on the genome of Bactrian camels was by Liang Ming from Inner Mongolia Agricultural University, China, and focused on the data obtained by resequencing-assembly of multiple Bactrian genomes for the development of genetic markers for both the domestic and wild populations. We learned that the wild Bactrian camel is more endangered than the Giant Panda. Mark Richardson from Deakin University, Australia, gave a progress report on the status of VicPac3.0 – an improved alpaca genome assembly achieved by incorporating 100X Illumina, 5X PacBio, and RNAseq data to the currently available VicPac2. The improved assembly is currently available at Deakin University server but the plan is to submit it to NCBI later in 2017. Felipe Avila from the University of Minnesota summarized the status of the cytogenetic map and integrated map data in camelids. To illustrate the application of molecular markers in camelid clinical cytogenetics, Felipe presented a case report of a sterile male llama carrying an autosomal translocation. The last talk was by Petr Hořín from the Brno Veterinary and Pharmaceutical University, Czech Republic, about sequence polymorphism of the MHC in Old World camelids.
Elections: Dr. Pamela Burger will serve as the Chair for PAG2018 Camelid Workshop with assistance from Dr. Don Miller (chair-elect for 2019).
Discussion (Panel: Samantha Brooks, Pamela Burger, Mark Richardson, Terje Raudsepp)
• FAANG: Possibility to include camelids in FAANG. Laura Clark from EMBL-EBI said that they can house data, either freely or hold until publication. She advised
to select tissues carefully, with the priority of high expression tissues, such as brain, testis, ovary. Suggested to avoid tissue overlap unless specific conditions of interest are identified. All in all, do as many tissues as possible and choose technology with long reads (iso-seq). Laura encouraged everyone continue with their current projects but advised to consider FAANG standards for the new ones. Importantly, we need to identify potential funding sources, e.g., national research foundations, Morris Animal Foundation, USDA?
• Phenotypes. Discussion about how and which camelid phenotypes to collect. Hasan Alhaddad from Kuwait University has made an iOS application “SamplEase” to facilitate sample collection in fieldwork settings. The app allows acquisition of basic data, including phtos. A recently EU funded project (Coordinator Prof. Juan Vicente Delgado Bermejo, University of Cordoba, Spain) is already collecting meat, milk and disease resistance phenotypes from dromedaries in Tunesia, Morocco, Algeria aiming for 2000 samples.
• Complex genomic regions and BAC library: in order to properly assemble complex genomic regions, for example, those harboring immunity related genes, a need for a dromedary genomic BAC library was discussed. Currently, the only BAC library in camelids is that of a female alpaca (CHORI-246). Questions: can alpaca BACs be used for sequence capture in the dromedary? Can 10X Genomics and Dovetail Genomics solve the assembly problems without BACs? Funding?
• Sweet dreams: Like everybody else, participants of the Camelid Workshop had great hopes that 10X Genomics and Dovetail Genomics will solve all their problems.
The day after:
• Sam Brooks brought a message from Jim Reecy that Animalgenome.org will be happy to host some large camelids datasets in their repository (we will get our own folder): http://www.animalgenome.org/repository/. Perhaps Mark Richardson et al would be interested to share the alpaca data there; Sam Brooks and Heather Holl will deposit a draft dromedary assembly.
• A small group (Pamela Burger, Doug Antczak, Petr Horin, Polina Perelman, Don Miller, Ernie Bailey and Terje Raudsepp) continued discussions about the best strategies for sequencing, assembly and study of immunity related genes (NK family) and MHC in camelids.
• Additional discussions (Polina Perelman, Mark Richardson, Denis Larkin, Pamela Burger, Terje Raudsepp) about publishing the alpaca 4000-marker RH map and its application to improve genome assembly. Also, discussions about sequencing clones from the recently constructed dromedary 5000rad and 15000rad RH panels – for improving dromedary sequence assembly and anchoring to chromosomes.
• Possibility to include camelids in NRSP8?
Finally and most importantly, in an effort to help us stay connected, last year Sam Brooks started a contact list for the workshop. The list is shared as a GoogleDoc and can be edited by anyone. Please feel free to correct your information and forward the link to whomever may wish to add themselves to the list. I already included new names from the 2017 workshop participants list.
Camelids Genome Workshop Contact List: https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
Once again, many, many thanks to all! Special thanks to Sam Brooks and Pamela Burger for taking meticulous notes during the workshop.
Have a happy and productive year 2017,
Terje
Terje Raudsepp, Ph.D; Associate Professor
Director of Molecular Cytogenetics Laboratory
Department of Veterinary Integrative Biosciences
College of Veterinary Medicine & Biomedical Sciences
Texas A&M University
488 Raymond Stotzer Pkw, VRB Room #314
The first Camelids Genomic Workshop at the XXIV PAG was organized by Samantha Brooks, Department of Animal Science, University of Florida:
Camelids Workshop Summary- 2016 Plant and Animal Genome Conference
Thanks to the many wonderful participants who made our Camelids workshop a great success. I was very impressed with the quality of the presentations and the collegial atmosphere of the group. I expect many new and exciting collaborations will result. During the two hour session we had approximately 45 participants from institutions around the world.
In an effort to help us stay connected I have started a contact listing for the workshop. This is currently shared as a GoogleDoc, though this admittedly may be a temporary solution. The GoogleDoc is editable, please feel free to correct your information, and forward broadly to whomever may wish to add themselves to the list.
Camelids Genome Workshop Contact List: https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
The session, held on Saturday January 9th, opened with a presentation from Pamela Berger on their work studying the origins of domestication in old world camels. Dr. Berger also highlighted the activities of the (The International Camel Consortium for genetic improvement and conservation) ICC-GIS, part of the larger The International Society of Camelid Research and Development (ISOCARD) organization.
http://www.isocard.net/images/announcements//FILE0fa335accbce997.pdf
Dr. Faisal Almathen also presented, relaying some of the findings from his mtDNA and msat study of ~1100 dromedary camels from diverse locations. Dr. Heather Holl relayed preliminary findings on the use of GBS for genotyping of dromedaries, and ongoing work to generate an improved dromedary reference assembly. Dr. David Murphy described his transcriptome work, aimed at better understanding unique adaptations for urine concentration in camels. New world camelids came to the forefront in a presentation by Dr. Terje Raudsepp on efforts to improve physical maps and assembly in the Alpaca. Finally, we heard a description of key coat color loci in the Alpaca genome; a very important economic trait for the fiber industry.
A discussion session held at the end of the meeting highlighted several “critical needs” for ongoing collaborative efforts. This included:
· Continuing RH-mapping efforts, especially for dromedaries
· Additional bioinformatics support
o Dr. Leslie Lyons recommended Maverix Biomics as a data sharing platform
· Need for a reference populations, perhaps with trios for phasing and as a tissue resource for transcriptomics
· Some suggested standards regarding the method and read depth for re-sequenced genomes
· Max Rothschild strongly supports development of a genotyping array, either illumina or affy, through GeneSeek. SNP discovery efforts underway now should provide sufficient markers.
· Organization and collaboration will be “key!”
The session concluded with election of Workshop Chairs for future PAG conferences. Dr. Terje Raudsepp will serve in 2017, with assistance from Dr. Pamela Berger (chair-elect for 2018).
Given the excellent comments at the conclusion of the workshop, a second informal brainstorming session convened on Tuesday January 12th at 8:30 pm.
· Communication and web resources are needed
o A network similar to the EvolDir site (http://life.mcmaster.ca/evoldir.html) would be nice
o A monthly email newletter including news, opening positions, offers of shared reagents, dates for upcoming meetings etc.
o A directory of researchers (perhaps though the ISO-CARD site)
o A central listing of what sequences are available where
· Additional RH mapping work will be completed by Paulina Pearlman with FAO-IAEA support (Berger group)
· For next years workshop, most agreed that 220 min talks are sufficient, and should come from PIs, Post-Docs and mature students. It was suggested that one invited “key note” speaker might be good. Poster sessions continue to be a great venue for younger graduate students.
· Is there a standardized karyotype for the dromedary? No, but Terje is working on some possible solutions. Scaffolds from assemblies might be anchored by sequence homology to references from species with zoo-FISH data in alpaca.
· Max Rothschild related that a Alpaca SNP chip is underway
· Funding possibilities
o A “RICE” call, an EU networking grant, is currently out. Pamela Berger volunteered to led a potential application here for meetings and collaborative resources.
o FAO may support breeding and phenotyping activities, population genetics might be fundable through these programs
o Gates foundation is currently not interested, perhaps due to a misconception that the camel is only agriculturally important to the Arabian peninsula
o Morris Animal has funded some Alpaca and may consider camel
o USAID may be a good program to consider, more will be coming soon from the new Livestock Innovation Lab housed at University of Florida
o Cooperative grant programs exist for Arab-Israeli and US-Egypt collaborations
· A periodic skype session is suggested by Ahmed Elbeltagi by email, these might be coordinated through a periodic email newsletter.
Given these suggestions, I will volunteer to draft a quarterly e-newsletter, though I am happy to hand this off to any volunteers willing to take on the task! Long-term, it might make sense to rotate this task with the elected chair for the PAG workshop.
Thanks for sharing your work, and your thoughts! I will look forward to seeing you all again soon at our next meeting! -SB
Camelids Workshop Summary- 2016 Plant and Animal Genome Conference
Thanks to the many wonderful participants who made our Camelids workshop a great success. I was very impressed with the quality of the presentations and the collegial atmosphere of the group. I expect many new and exciting collaborations will result. During the two hour session we had approximately 45 participants from institutions around the world.
In an effort to help us stay connected I have started a contact listing for the workshop. This is currently shared as a GoogleDoc, though this admittedly may be a temporary solution. The GoogleDoc is editable, please feel free to correct your information, and forward broadly to whomever may wish to add themselves to the list.
Camelids Genome Workshop Contact List: https://docs.google.com/spreadsheets/d/1TUlp3xXpQe403NPOE43GobfzPVhnCgm9pBBq6FXYjys/edit?usp=sharing
The session, held on Saturday January 9th, opened with a presentation from Pamela Berger on their work studying the origins of domestication in old world camels. Dr. Berger also highlighted the activities of the (The International Camel Consortium for genetic improvement and conservation) ICC-GIS, part of the larger The International Society of Camelid Research and Development (ISOCARD) organization.
http://www.isocard.net/images/announcements//FILE0fa335accbce997.pdf
Dr. Faisal Almathen also presented, relaying some of the findings from his mtDNA and msat study of ~1100 dromedary camels from diverse locations. Dr. Heather Holl relayed preliminary findings on the use of GBS for genotyping of dromedaries, and ongoing work to generate an improved dromedary reference assembly. Dr. David Murphy described his transcriptome work, aimed at better understanding unique adaptations for urine concentration in camels. New world camelids came to the forefront in a presentation by Dr. Terje Raudsepp on efforts to improve physical maps and assembly in the Alpaca. Finally, we heard a description of key coat color loci in the Alpaca genome; a very important economic trait for the fiber industry.
A discussion session held at the end of the meeting highlighted several “critical needs” for ongoing collaborative efforts. This included:
· Continuing RH-mapping efforts, especially for dromedaries
· Additional bioinformatics support
o Dr. Leslie Lyons recommended Maverix Biomics as a data sharing platform
· Need for a reference populations, perhaps with trios for phasing and as a tissue resource for transcriptomics
· Some suggested standards regarding the method and read depth for re-sequenced genomes
· Max Rothschild strongly supports development of a genotyping array, either illumina or affy, through GeneSeek. SNP discovery efforts underway now should provide sufficient markers.
· Organization and collaboration will be “key!”
The session concluded with election of Workshop Chairs for future PAG conferences. Dr. Terje Raudsepp will serve in 2017, with assistance from Dr. Pamela Berger (chair-elect for 2018).
Given the excellent comments at the conclusion of the workshop, a second informal brainstorming session convened on Tuesday January 12th at 8:30 pm.
· Communication and web resources are needed
o A network similar to the EvolDir site (http://life.mcmaster.ca/evoldir.html) would be nice
o A monthly email newletter including news, opening positions, offers of shared reagents, dates for upcoming meetings etc.
o A directory of researchers (perhaps though the ISO-CARD site)
o A central listing of what sequences are available where
· Additional RH mapping work will be completed by Paulina Pearlman with FAO-IAEA support (Berger group)
· For next years workshop, most agreed that 220 min talks are sufficient, and should come from PIs, Post-Docs and mature students. It was suggested that one invited “key note” speaker might be good. Poster sessions continue to be a great venue for younger graduate students.
· Is there a standardized karyotype for the dromedary? No, but Terje is working on some possible solutions. Scaffolds from assemblies might be anchored by sequence homology to references from species with zoo-FISH data in alpaca.
· Max Rothschild related that a Alpaca SNP chip is underway
· Funding possibilities
o A “RICE” call, an EU networking grant, is currently out. Pamela Berger volunteered to led a potential application here for meetings and collaborative resources.
o FAO may support breeding and phenotyping activities, population genetics might be fundable through these programs
o Gates foundation is currently not interested, perhaps due to a misconception that the camel is only agriculturally important to the Arabian peninsula
o Morris Animal has funded some Alpaca and may consider camel
o USAID may be a good program to consider, more will be coming soon from the new Livestock Innovation Lab housed at University of Florida
o Cooperative grant programs exist for Arab-Israeli and US-Egypt collaborations
· A periodic skype session is suggested by Ahmed Elbeltagi by email, these might be coordinated through a periodic email newsletter.
Given these suggestions, I will volunteer to draft a quarterly e-newsletter, though I am happy to hand this off to any volunteers willing to take on the task! Long-term, it might make sense to rotate this task with the elected chair for the PAG workshop.
Thanks for sharing your work, and your thoughts! I will look forward to seeing you all again soon at our next meeting! -SB
