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Can genomics (help) save California’s biodiversity?

Brad Shaffer

UCLA

PAG XXIX | January 10th, 2022

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What is the conservation genomics community currently doing?

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  • Large multi-species projects (VGP, EBP)
    • High-quality reference genomes
    • Single exemplars only

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  • Single species projects
    • Population-level sampling and analysis
    • Usually with partial (RADseq) data

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CCGP goals

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  • Taxonomic and ecological coverage for the state, replicated across many species
  • Develop meaningful statewide landscape genomic maps:
      • Hotspots: multispecies, climate-resilient
      • Corridors: to connect hotspots
      • Critical lands: to acquire and protect

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CCGP at a glance:

  • ~247 species in ~150 projects
  • Comprehensive landscape genomic dataset
    • One high quality reference genome for all 150 projects
    • Whole genome resequencing (WGS) for ~20,000 individuals
    • Best available landscape GIS/imagery
  • Data for management/policy:
    • State and federal agencies
    • Private and public land managers

The California Conservation Genomics Project (CCGP)

A collaborative effort to conserve California flora and fauna using conservation & landscape genomics of threatened, commercially exploited and ecologically important species.

For more info:

ccgproject.org

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The Team

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  • 79 Principal Investigators
  • All 10 UC campuses
  • Executive committee includes 5 UC’s, CDFW, USFWS, Governor’s office
  • Several hundred co-PI’s
  • California Dept. of Food & Ag (pest spp.)

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Details

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  • $12 M from the state budget
  • ~$10 M goes directly out to labs
  • All data must be consistent:
    • Reference genomes done by CCGP
    • Resequencing (WGS) to maximize landscape coverage across the state
  • Conservation relevance

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Phylogenetic coverage:

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Group

#

Group

#

amphibian

3

marine fish

7

bird

17

marine invertebrate

11

fish

5

marine mammal

2

herbaceous plant

24

marine plant

2

invertebrate

19

reptile

16

mammal

13

tree

10

Taxon rank

Lineages covered

phyla

8

classes

22

orders

66

families

100

genera

121

species

148

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Reference genome progress

Number of Species Completed (as of January 7th, 2022)

  • 148 species expected
  • Almost all tissues assembled
  • Lab component complete for >75%
  • Data available for half of the tissues processed

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  • Karyotype 2n=50 (26 Macro/24 micro)
  • 3 SMRT Cells: ~ 30X
  • Estimated genome size: 2.6 Gb (Final 2.3 Gb)
    • Heterozygosity ~0.4%
  • Chromosome-level assembly (with curation)
  • Contig N50 75 Mb, Scaffold N50 146 Mb
  • Largest contig 223 Mb, Largest scaffold 361 Mb

Northwestern pond turtle

Actinemys marmorata

Merqury (kmer) analysis

P

A

K-mer compleness

ASM

92.881

88.2501

FULL

99.0156

base-call QV

ASM

66.5877

65.4596

FULL

66.0007

BUSCO Scores (n=3,354; vertebrata)*

ASM

C

S

D

F

M

P

96.70%

95.80%

0.90%

0.90%

2.40%

A

91.20%

89.90%

1.30%

1.50%

7.30%

Merly Escalona

UCSC

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  • First complete genome (and paper)
    • Yuang, Escalona et al. 2021, J. of Heredity
  • 1 SMRT Cell: ~45.5X
  • Estimated genome size: 0.5 Gb
  • Highly repetitive (>50%) and highly heterozygous ~2.51%
  • Dovetail’s HiC data: 199M read pairs; 2x150 bp

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Bigberry manzanita

Arctostaphylos glauca

General statistics

Primary

Alternate

Length of genome

547,548,103

556,397,040)

# Sequences (contigs/scaffolds)

353/271

2,470/2,350

Contig N50

8,041,760

1,739,008

Contig L50

19

80

Longest contig

22,990,225

10,884,557

Scaffold N50

31,280,158

3,804,428

Scaffold L50

7

32

Longest scaffold

45,401,621

22,987,546

# Gaps

150

1,885

Merqury (kmer) analysis

P

A

base-call QV

ASM

62.36

56.24

FULL

58.28

k-mer completeness

ASM

74.396

65.0156

FULL

95.5926

BUSCO (v5) Scores (n=1614, embryophyta)*

ASM

C

S

D

F

M

P

98.20%

95.70%

2.50%

0.90%

0.90%

A

87.90%

83.30%

2.60%

1.30%

12.80%

(C)omplete and (S)ingle | (C)omplete and (D)uplicated

(F)ragmented | (M)issing

Frame shift error analysis (*)

P

A

Indel QV

48.38

47.39

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19 USDA Ecoregions

Marine

Plant

Vertebrate

Invertebrate

WGS: Sampling

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WGS: Ecoregion coverage

# samples

(# projects)

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Whole Genome Resequencing Progress

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  • Established a new UCLA core facility for benchwork
  • Out of 10,000 expected samples:
            • Samples received: 3540
            • Extracted: 1729
            • Completed: 1195
  • Many labs doing their own work

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Data Analysis

  • All data analyzed by CCGP team & independently by PI
  • CCGP informatics team
    • Russ Corbett-Detig lead (UCSC)
    • Erik Enbody postdoc
    • Cade Merchandani data wrangler
  • CCGP landscape genomics team
    • Ian Wang (UC Berkeley)
    • Anne Chambers postdoc

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End Game Deliverables

  • We’re into Year 3
  • Reference genomes complete: May 2022
  • WGS complete: October 2022
  • Work with state regulatory agencies, CA 30x30, NGO community
    • Identify most resilient landscapes for protection
    • Hire outreach coordinator to optimize impact

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Acknowledgements

  • CCGP team (past and present)
    • Brad Shaffer, Victoria Sork, Erin Toffelmier, Bjorn Erickson,

Peggy Fiedler, Mark Gold, Scott Hodges, Kevin Shaffer, Ian Wang, Lutz Froenicke, Christopher Hann-Soden, Harris Lewin, Ryan Harrigan, Stephen Richards, Courtney Miller, Daniel Oliveira, Tara Luckau,

Russ Corbett-Detig, Erik Enbody, Cade Mirchandani, Anne Chambers

  • CCGP PIs & teams
  • UCSC Paleogenomics Lab
    • Beth Shapiro, Ed Green, Sam Sacco, Eric Beraut, Colin Fairbairn, Will Seligmann
  • UCD Genome Center
    • Oanh Nguyen, Ruta Sahasrabudhe, Mohan Prem Anand Marimuthu,

Noravit Chumchim, Lutz Froenicke

  • PacBio
    • Jonas Korlach, Michelle Vierra, Matt Settin, John Alterio