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Genetic variation of Colletotrichum spp. causing leaf anthracnose disease in citrus (Citrus spp.) on Java, Indonesia

JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA · Vol. 26 No. 2 (2026) · pp. 602–614

DOI
10.23960/j.hptt.226602-614
ISSN
2461-0399, 1411-7525
Published
2026-09-22
Publisher
Universitas Lampung
Language
eng
License
creativecommons.org/licenses/by-nc/4.0

Abstract

Citrus is an important horticultural commodity in Indonesia, particularly for fresh consumption and as a raw material for processed products. Anthracnose caused by Colletotrichum spp. is an important disease of citrus that can substantially affect plant health and productivity. However, information on the diversity and identity of Colletotrichum species associated with citrus anthracnose in Java, Indonesia, remains limited. In this study, twelve Colletotrichum isolates were obtained from citrus leaves showing anthracnose symptoms collected from several citrus-growing regions in Java. The isolates were characterized based on morphological characteristics and genetic fingerprinting using repetitive element sequence-based PCR (rep-PCR) with BOX and ERIC primers. Seven representative isolates were subsequently selected for multilocus molecular identification and phylogenetic analysis based on partial sequences of five loci: internal transcribed spacer (ITS), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-tubulin (TUB2), and Apn2-Mat1-2 intergenic spacer (ApMat). The multilocus phylogenetic analysis placed the representative isolates into two major lineages corresponding to Colletotrichum siamense and the C. gloeosporioides species complex. Morphological characteristics were generally consistent with their molecular placement, although considerable overlap was observed among isolates. Pathogenicity assays on detached citrus leaves showed that all representative isolates produced anthracnose-like lesions, with differences in lesion development among isolates. These findings demonstrate the occurrence of genetically and phenotypically variable Colletotrichum isolates associated with citrus leaf anthracnose in Java and provide baseline information for further studies on pathogen diversity and disease management.

Keywords

Collaboration network of the authors

40 authors · 126 co-authorship links · showing the 40 most connected

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  • Diponegoro University
  • Affiliation unknown
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Co-authorOrganisationJoint articles
Siti SubandiyahAffiliation unknown7
Tri JokoDiponegoro University6
Stephen HarperAffiliation unknown3
Danar WicaksonoAffiliation unknown2
Islaminati Anna SantikaAffiliation unknown2
Luthfiana Mifta SyafitriAffiliation unknown2
Annisa Hasta PratiwiAffiliation unknown2
Muhammad HabibullahAffiliation unknown2
Wahyu Sandra AnggariniAffiliation unknown1
Rihab Wit DaryonoAffiliation unknown1
Syariful MubarokAffiliation unknown1
Cory RafsyanyaniAffiliation unknown1
Titah Rigel AnjalaniAffiliation unknown1
Anisa Esti RahayuAffiliation unknown1
Deden Derajat MatraAffiliation unknown1
Hiroshi EzuraAffiliation unknown1
Nurul JadidAffiliation unknown1
Barokati TsaniyahAffiliation unknown1
Endang SulistyaningsihAffiliation unknown1
Rachmanto Bambang WijoyoAffiliation unknown1
Widya Pintaka Bayu PutraAffiliation unknown1
Anang Hari KristantoAffiliation unknown1
Budi SetyawanAffiliation unknown1
Valérie Pujade-RenaudAffiliation unknown1
Siti Muslimah WidyastutiAffiliation unknown1
Christanti SumardiyonoAffiliation unknown1
Johanna TaribukaAffiliation unknown1
Auliana AfandiAffiliation unknown1
MasantoAffiliation unknown1
AfandiAffiliation unknown1
Supriyono LoekitoAffiliation unknown1
Ayaka HienoAffiliation unknown1
Kayako OtsuboAffiliation unknown1
Kageyama KojiAffiliation unknown1
Hurin Nabila Aghnia IlmaAffiliation unknown1
Hoerussalam HoerussalamAffiliation unknown1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) http://jhpttropika.fp.unila.ac.id/index.php/jhpttropika/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (oai_dc) 
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	<dc:title xml:lang="en">Genetic variation of Colletotrichum spp. causing leaf anthracnose disease in citrus (Citrus spp.) on Java, Indonesia</dc:title>
	<dc:creator xml:lang="en">Salma, Nabila Khairunnisa </dc:creator>
	<dc:creator xml:lang="en">Widiastuti, Ani </dc:creator>
	<dc:creator xml:lang="en">Nurlaelita, Khaerani </dc:creator>
	<dc:creator xml:lang="en">Wibowo, Arif</dc:creator>
	<dc:subject xml:lang="en">Anthracnose</dc:subject>
	<dc:subject xml:lang="en">citrus</dc:subject>
	<dc:subject xml:lang="en">Colletotrichum gloeosporioides</dc:subject>
	<dc:subject xml:lang="en">Colletotrichum siamense</dc:subject>
	<dc:subject xml:lang="en">genetic diversity</dc:subject>
	<dc:subject xml:lang="en">multilocus phylogeny</dc:subject>
	<dc:subject xml:lang="en">species complex</dc:subject>
	<dc:description xml:lang="en">Citrus is an important horticultural commodity in Indonesia, particularly for fresh consumption and as a raw material for processed products. Anthracnose caused by Colletotrichum spp. is an important disease of citrus that can substantially affect plant health and productivity. However, information on the diversity and identity of Colletotrichum species associated with citrus anthracnose in Java, Indonesia, remains limited. In this study, twelve Colletotrichum isolates were obtained from citrus leaves showing anthracnose symptoms collected from several citrus-growing regions in Java. The isolates were characterized based on morphological characteristics and genetic fingerprinting using repetitive element sequence-based PCR (rep-PCR) with BOX and ERIC primers. Seven representative isolates were subsequently selected for multilocus molecular identification and phylogenetic analysis based on partial sequences of five loci: internal transcribed spacer (ITS), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-tubulin (TUB2), and Apn2-Mat1-2 intergenic spacer (ApMat). The multilocus phylogenetic analysis placed the representative isolates into two major lineages corresponding to Colletotrichum siamense and the C. gloeosporioides species complex. Morphological characteristics were generally consistent with their molecular placement, although considerable overlap was observed among isolates. Pathogenicity assays on detached citrus leaves showed that all representative isolates produced anthracnose-like lesions, with differences in lesion development among isolates. These findings demonstrate the occurrence of genetically and phenotypically variable Colletotrichum isolates associated with citrus leaf anthracnose in Java and provide baseline information for further studies on pathogen diversity and disease management.</dc:description>
	<dc:publisher xml:lang="en">Universitas Lampung</dc:publisher>
	<dc:date>2026-09-22</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://jhpttropika.fp.unila.ac.id/index.php/jhpttropika/article/view/917</dc:identifier>
	<dc:identifier>10.23960/j.hptt.226602-614</dc:identifier>
	<dc:source xml:lang="en">Jurnal Hama dan Penyakit Tumbuhan Tropika; Vol. 26 No. 2 (2026): SEPTEMBER, JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA: JOURNAL OF TROPICAL PLANT PESTS AND DISEASES; 602-614</dc:source>
	<dc:source>2461-0399</dc:source>
	<dc:source>1411-7525</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://jhpttropika.fp.unila.ac.id/index.php/jhpttropika/article/view/917/733</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2026 Jurnal Hama dan Penyakit Tumbuhan Tropika</dc:rights>
	<dc:rights xml:lang="en">https://creativecommons.org/licenses/by-nc/4.0</dc:rights>
</oai_dc:dc>