Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)

Aireen Suet Lin Phang; Flávia Fonseca Pezzini; David Burslem; Gillian S W Khew; Gillian S W Khew; David John Middleton; Markus  Ruhsam; P. Wilkie

doi:10.1093/botlinnean/boad022

Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)

Aireen Suet Lin Phang^* (Corresponding Author), Flávia Fonseca Pezzini, David Burslem, Gillian S W Khew, Gillian S W Khew, David John Middleton, Markus Ruhsam, P. Wilkie

^*Corresponding author for this work

Biological Sciences

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Abstract

The first phylogenomic study using a custom target capture bait panel within the Isonandreae tribe in Sapotaceae is presented. The combination of taxon-specific and universal loci from the Angiosperms353 probe set achieved high species resolution within the genus Palaquium and provides the first phylogenomic insights into Malesian representatives of Sapotaceae, where relationships between taxa often remain poorly understood. The results highlight that generic and some species circumscriptions require further investigation and possible revision: Aulandra longifolia is found to be nested in Palaquium, and P. rostratum within P. microphyllum. Population structure analysis produced limited resolution between and within species, but the bait set was able to recover parameters that are potentially useful in population genomic studies.

Original language	English
Pages (from-to)	134-147
Number of pages	14
Journal	Botanical Journal of the Linnean Society
Volume	203
Issue number	2
Early online date	6 Jul 2023
DOIs	https://doi.org/10.1093/botlinnean/boad022
Publication status	Published - Oct 2023

Bibliographical note

ACKNOWLEDGEMENTS
We thank the management of the National Parks Board and Singapore Botanic Gardens for providing continuous support, facilities and fieldwork approval in Singapore’s nature reserves. We appreciate the digital research team at the University of Aberdeen and the research/scientific computing teams at The James Hutton Institute and NIAB for providing technical support while using the computational resources on the respective HPC clusters, “Maxwell” and the “UK Crop Diversity Bioformatics HPC” (BBSRC grant BB/S019669/1), which have contributed to the results within this paper. We thank numerous staff at the Singapore Botanic Gardens, particularly Khoo-Woon Mui Hwang and Neo Wei Ling for strong technical support in the molecular lab, Matti Niissalo for generous sharing of lab protocols and bioinformatics tips, Choo Le Min for patient help with lab troubleshooting, Chong Kwek Yan and Chan Pin Jia for forest survey expertise, and Louise Neo for thoughtful field and R advice.
Our sincere thanks are due to Herbarium staff at the Royal Botanic Garden Edinburgh, including Lesley Scott, for efficient assistance in sending silica-dried samples to the Singapore Botanic Gardens. We also thank Camille Christe at the Conservatoire et Jardin botaniques de la Ville de Genève for kind advice related to the taxon-specific baits’ setup and purchase

FUNDING
We are grateful to the Lady Yuen Peng McNeice Charitable Foundation for financial support of this study.

Data Availability Statement

DATA AVAILABILITY
Raw sequence data (Table S1 in the Supporting Information) are available from National Center for Biotechnology Information under the Bioproject number PRJNA912780:https://www.ncbi.nlm.nih.gov. (NB. to be released on publication)

Keywords

Molecular systematics
Palaquium
Population genomics
Sapotaceae
Southeast Asia
target capture

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Cite this

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title = "Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)",

abstract = "The first phylogenomic study using a custom target capture bait panel within the Isonandreae tribe in Sapotaceae is presented. The combination of taxon-specific and universal loci from the Angiosperms353 probe set achieved high species resolution within the genus Palaquium and provides the first phylogenomic insights into Malesian representatives of Sapotaceae, where relationships between taxa often remain poorly understood. The results highlight that generic and some species circumscriptions require further investigation and possible revision: Aulandra longifolia is found to be nested in Palaquium, and P. rostratum within P. microphyllum. Population structure analysis produced limited resolution between and within species, but the bait set was able to recover parameters that are potentially useful in population genomic studies. ",

keywords = "Molecular systematics, Palaquium, Population genomics, Sapotaceae, Southeast Asia, target capture",

author = "Phang, {Aireen Suet Lin} and Pezzini, {Fl{\'a}via Fonseca} and David Burslem and Khew, {Gillian S W} and Khew, {Gillian S W} and Middleton, {David John} and Markus Ruhsam and P. Wilkie",

note = "ACKNOWLEDGEMENTS We thank the management of the National Parks Board and Singapore Botanic Gardens for providing continuous support, facilities and fieldwork approval in Singapore{\textquoteright}s nature reserves. We appreciate the digital research team at the University of Aberdeen and the research/scientific computing teams at The James Hutton Institute and NIAB for providing technical support while using the computational resources on the respective HPC clusters, “Maxwell” and the “UK Crop Diversity Bioformatics HPC” (BBSRC grant BB/S019669/1), which have contributed to the results within this paper. We thank numerous staff at the Singapore Botanic Gardens, particularly Khoo-Woon Mui Hwang and Neo Wei Ling for strong technical support in the molecular lab, Matti Niissalo for generous sharing of lab protocols and bioinformatics tips, Choo Le Min for patient help with lab troubleshooting, Chong Kwek Yan and Chan Pin Jia for forest survey expertise, and Louise Neo for thoughtful field and R advice. Our sincere thanks are due to Herbarium staff at the Royal Botanic Garden Edinburgh, including Lesley Scott, for efficient assistance in sending silica-dried samples to the Singapore Botanic Gardens. We also thank Camille Christe at the Conservatoire et Jardin botaniques de la Ville de Gen{\`e}ve for kind advice related to the taxon-specific baits{\textquoteright} setup and purchase FUNDING We are grateful to the Lady Yuen Peng McNeice Charitable Foundation for financial support of this study. ",

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AU - Phang, Aireen Suet Lin

AU - Pezzini, Flávia Fonseca

AU - Burslem, David

AU - Khew, Gillian S W

AU - Middleton, David John

AU - Ruhsam, Markus

AU - Wilkie, P.

N1 - ACKNOWLEDGEMENTS We thank the management of the National Parks Board and Singapore Botanic Gardens for providing continuous support, facilities and fieldwork approval in Singapore’s nature reserves. We appreciate the digital research team at the University of Aberdeen and the research/scientific computing teams at The James Hutton Institute and NIAB for providing technical support while using the computational resources on the respective HPC clusters, “Maxwell” and the “UK Crop Diversity Bioformatics HPC” (BBSRC grant BB/S019669/1), which have contributed to the results within this paper. We thank numerous staff at the Singapore Botanic Gardens, particularly Khoo-Woon Mui Hwang and Neo Wei Ling for strong technical support in the molecular lab, Matti Niissalo for generous sharing of lab protocols and bioinformatics tips, Choo Le Min for patient help with lab troubleshooting, Chong Kwek Yan and Chan Pin Jia for forest survey expertise, and Louise Neo for thoughtful field and R advice. Our sincere thanks are due to Herbarium staff at the Royal Botanic Garden Edinburgh, including Lesley Scott, for efficient assistance in sending silica-dried samples to the Singapore Botanic Gardens. We also thank Camille Christe at the Conservatoire et Jardin botaniques de la Ville de Genève for kind advice related to the taxon-specific baits’ setup and purchase FUNDING We are grateful to the Lady Yuen Peng McNeice Charitable Foundation for financial support of this study.

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AB - The first phylogenomic study using a custom target capture bait panel within the Isonandreae tribe in Sapotaceae is presented. The combination of taxon-specific and universal loci from the Angiosperms353 probe set achieved high species resolution within the genus Palaquium and provides the first phylogenomic insights into Malesian representatives of Sapotaceae, where relationships between taxa often remain poorly understood. The results highlight that generic and some species circumscriptions require further investigation and possible revision: Aulandra longifolia is found to be nested in Palaquium, and P. rostratum within P. microphyllum. Population structure analysis produced limited resolution between and within species, but the bait set was able to recover parameters that are potentially useful in population genomic studies.

KW - Molecular systematics

KW - Palaquium

KW - Population genomics

KW - Sapotaceae

KW - Southeast Asia

KW - target capture

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DO - 10.1093/botlinnean/boad022

M3 - Article

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JO - Botanical Journal of the Linnean Society

JF - Botanical Journal of the Linnean Society

IS - 2

ER -

Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)

Abstract

Bibliographical note

Data Availability Statement

Keywords

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